Michel Espinoza-Fonseca: "Re: Vibrational. edu) Date: Tue Aug 04 2009 - 00:36:38 CDT Next message: Nicholas M Glykos: "Re: A script for performing calculations divided by quanta" Previous message: Joshua Adelman: "Re: A script for performing calculations divided by quanta". Gianluca Interlandi. > > NCSA Forge has for example 6 CUDA devices and 16 CPU cores per node. edu> > wrote: > are other people also using those GPUs? > >In reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. Re: NAMD 2. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. New UW Bioengineering research assistant professor Gianluca Interlandi studies the molecular function of blood proteins involved in hemostasis and clotting. (2010) The catch bond mechanism between von Willebrand factor and platelet surface receptors investigated by molecular dynamics simulations. You simply load your trajectory > > into VMD On 7/7/2011 6:08 PM, Gianluca Interlandi wrote: > Francesco, > > Just a hint. 0 and 2. uiuc. edu> wrote: > Hi, > > Can the current version of NAMD be used together with the new CHARMM36 force > field? The parameter files are "top_all36_prot. 1002/prot. edu) Date: Thu Feb 20 2014 - 13:15:51 CST Next message: zeynab mohamad hoseyni: "FATAL ERROR: EOF ENCOUNTERED READING CROSS-TERMS FROM PSF FILE" Previous message: Kenno Vanommeslaeghe: "Re: tools for Charmm" In reply to: Kenno Vanommeslaeghe: "Re:. 6 version, although I am not running the cluster at full load yet. > You could build a PC with the Asus p5Q Pro Motherboard, Intel Quadcore Q8200 > and two GTX 285 cards for under 900$ (plus the cost of the usual PC > components). washington. washington. 26588 Item in Clipboard Cite. Sarah Keller Professor. I would be > happy if somebody could point me out to some scripts which help me performHemostasis in vertebrates involves both a cellular and a protein component and von Willebrand factor evolved in the ancestral vertebrate following the divergence of the urochordates some 500 million years ago and that it acquired increasing complexity though sequential insertion of functional modules. unam. It's > slightly faster but still not that much faster than running on 16 CPU cores. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. washington. washington. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. Reply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] have you tried the multicore build? I wonder if the prebuilt smp one is just not working for you. washington. uiuc. edu) Date: Fri May 01 2009 - 12:18:05 CDT Next message: Grace Brannigan: "Re: crash with more than 96 processors (v2. Correspondence to: Gianluca Interlandi, Department of Bioengineering, University of Washington Box 355061, 3720 15th Ave NE, Seattle, WA 98195-5061, USA. SASA in NAMD is used internally > to perform simulations in implicit solvent, whereas SASA in VMD is used to > analyse trajectories. Reply: Gianluca Interlandi: "Re: Changing Boundary conditions from PBC to non-periodic" Messages sorted by: [ attachment ] Dear NAMD users, A portion of my protein is outside of the simulation box. VMD-L Mailing List. edu) Date: Mon May 28 2007 - 10:33:29 CDT Next message: Gianluca Interlandi: "Re: Protein in/out of box" Previous message: Peter Freddolino: "Re: constraints on zinc ions" In reply to: Monika Sharma: "Protein in/out of box" Next in. Next message: Gianluca Interlandi: "RE: Force field design" Previous message: Aron Broom: "Re: Force field design" In reply to: Abhishek TYAGI: "Force field design" Next in thread: Mayne, Christopher G: "Re: Force field design" Messages sorted by: [ attachment ] If you are familiar with the CHARMM program, a good resource is:. Anderson: "Re: rlwrap problem on" In reply to: Frank Barry: "rlwrap problem on" Next in thread: Gianluca Interlandi: "Re: rlwrap problem on" Reply:. Biochemistry. washington. washington. 6 : Tue Dec 27 2016 - 23:21:14 CST Gianluca Interlandi's 67 research works with 730 citations and 2,578 reads, including: Rate limiting step of the allosteric activation of the bacterial adhesin FimH investigated by molecular. rtf" and "par_all36_prot. }, author={Dagmara I. Pavel Aprikian, # 1 Gianluca Interlandi, # 2 Brian A. edu) Date: Wed Jul 16 2014 - 00:32:49 CDT Next message: Sadegh Faramarzi Ganjabad: "Re:Subject: Re: Subject: Re:Re: New partial charges after patching" Previous message: Gianluca Interlandi: "Re: Force field design" Next in. Does it also take account of the Urey-Bradley term? Many thanks, Gianluca ----- Gianluca Interlandi gianluca_at_bioc. washington. Proteins 78, 2506–2522 [PMC free article] [Google Scholar] > On Wed, 16 Sep 2020 at 11:40, Gianluca Interlandi <gianluca_at_u. Gianluca Interlandi Research Assistant Professor. Gianluca has 2 jobs listed on their profile. GianlucaHosted by Gianluca Interlandi. Cheers! If you are looking for Virtual General Counsel, please go to: out professional insights posted by Isabella Interlandi, Attorney at Law, Legal adviser, UNSC 1540 Committee former Expert, Customs legislation and procedures. Re: Abe versus Lincoln. Rachel Klevit WRF Endowed Chair in Biochemistry. Whitfield, 2 Esther Bullitt, 4 Ronald E. Cancellation policy. I would be > happy if somebody could point me out to some scripts which help me performOn Fri, Jun 27, 2008 at 9:16 PM, Gianluca Interlandi <gianluca_at_u. edu> wrote: >> blades generally tend to be a bit slower than "normal" nodes. 7 ns/day, which seems decent given the system size. Policies. SMD on center of mass. washington. Reply: Gianluca Interlandi: "Re: Cuda benchmarks namd2. 7 out the door on Friday. Reply: Gianluca Interlandi: "Re: Abe versus Lincoln" Messages sorted by: [ attachment ] Hi Gianluca, Using 4 Lincoln nodes with a 112580 atoms system I get 9. Here they are: a. Sarah Keller Professor. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build?Gianluca Interlandi composed on 2017-01-23 13:40 (UTC-0800):. I doubt that there is a way to have> On Thu, Apr 7, 2011 at 2:22 PM, Gianluca Interlandi > <gianluca_at_u. washington. , and Thomas W. I would be > happy if somebody could point me out to some scripts which help me performRe: checkpoint software for NAMD? From: Gianluca Interlandi (gianluca_at_u. July; 84 (7):990–1008. Reply: Gianluca Interlandi: "Re: query about wrapped coordinates" Messages sorted by: [ attachment ] Hi, Thanks again for your useful suggestions. Facebook gives people. Previous studies. The more tasks you have the > more frequently the CPUs need to update each other. edu) Date: Thu Nov 02 2006 - 15:40:40 CST Next message: Gianluca Interlandi: "Re: SMD on center of mass" Previous message: Ugur Akgun: "ABF on a single molecule" In reply to: Gianluca Interlandi: "Re: external force" Next in. g. I made those videos seven years ago. Stenkamp, 3 Wendy E. washington. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. edu) Date: Fri May 01 2009 - 12:18:05 CDT Next message: Grace Brannigan: "Re: crash with more than 96 processors (v2. > > Gianluca >Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"> On Thu, Dec 2, 2010 at 2:35 PM, Gianluca Interlandi <gianluca_at_u. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. In the text > field you can enter your atom selection, e. Contact host. Previous message: Gianluca Interlandi: "Re: Compiling NAMD 2. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. edu > Subject: Re: namd-l: DCD > > Load your psf+dcd into VMD. I was getting 2. washington. >Gianluca Interlandi (Property Manager Baroque Apartments) Hosting since October 2020. View all 11 amenities. We are building a smaller cluster though in the lab and will test the scalability2006/9/6, Gianluca Interlandi <gianluca_at_u. 7 released". edu] Sent: Thursday, April 05, 2012 5:04 PM To: Buddhadev Maiti Cc: Jérôme Hénin; namd-l_at_ks. edu> wrote:Reply: Gianluca Interlandi: "Re: Help building a desktop for namd" Messages sorted by: [ attachment ] On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi <gianluca_at_u. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). washington. E-mail: [email protected],. prm". washington. edu> wrote: > Hi, > > I have a question concerning running NAMD on a CUDA cluster. washington. washington. 25050 [PMC free article] [Google Scholar] EDUCATION<br><br>2012 November: WHR Seminar: Seminar about Hotel Revenue, web e social Marketing at Hotel Le Le Capannelle, Roma, Italy (Nov. From: Gianluca Interlandi (gianluca_at_u. On the other hand, a 4 TB WD 7200RPM is under 200$. From: Gianluca Interlandi (gianluca_at_u. washington. 7b1 on Abe" Previous message: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" In reply to: Gianluca Interlandi: "Re: Yet another. washington. Sunhwan On Jul 16, 2014, at 12:32 AM, Gianluca Interlandi <gianluca_at_u. These are the lastIn reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. Education/training Institution and location Dates attended Degree Conferred Field of study Interlandi G, Thomas WE. washington. VMD-L Mailing List. washington. 7 with the PLUMED patch" Messages sorted by: [ attachment ] I found the problem. The simulations were not performed at constant velocity > but at constant force. Re: query about wrapped coordinates. washington. washington. edu) Date: Thu Apr 05 2012 - 16:30:29 CDT Next message: Gianluca Interlandi: "RE: DCD" Previous message: Axel Kohlmeyer: "Re: DCD" In reply to: Buddhadev Maiti: "RE: DCD" Next in thread: Gianluca Interlandi: "RE: DCD" Reply: Gianluca Interlandi: "RE: DCD". Interlandi G. Next message: Gianluca Interlandi: "Infiniband and PME gridsize" Previous message: nordgren_at_sas. washington. From: Gianluca Interlandi (gianluca_at_u. washington. Gianluca On Thu, 6 Jan 2011, Gianluca Interlandi wrote: > Hi!In reply to: Gianluca Interlandi: "Re: Question about equilibration" Next in thread: Gianluca Interlandi: "Re: Question about equilibration" Reply: Gianluca Interlandi: "Re: Question about equilibration" Messages sorted by: [ attachment ] Because an X-ray is assumed to be a structure at "zero K" and an MD equilibrated. I would like to erase Windows and install Leap 42. Gianluca Interlandi Curriculum Vitae Department of Bioengineering, University of Washington, 1705 NE Pacific Street, 98195 Seattle, WA, [email protected]: Gianluca Interlandi (gianluca_at_u. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. Gianluca > Gianluca > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? I wonder if the prebuilt > smp one is just not > working for you. 6 ns/day for a 100k atom system with roughly those same parameters (and. edu> wrote: > Hi Fatemeh, > > Thanks for replying. You should simulate it in explicit water (or try one of the implicitGianluca Interlandi is on Facebook. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"From: Gianluca Interlandi (gianluca_at_u. (Oct-Nov 1997) Spanish: Fluent written and spoken German: Basic Knowledge WORK EXPERIENCE 2019 October: Founder Host. Comparative controls consisted of FocH (high affinity with and. washington. Display options Format Abstract The bacterial adhesin FimH is a model for the study of protein allostery because its structure has been resolved. , Thomas W. edu) Date: Thu Mar 17 2011 - 17:58:46 CDT Next message: Giacomo Fiorin: "Re: GBIS and ABF" Previous message: Branko: "GBIS and ABF" In reply to: Gianluca Interlandi: "Re: NAMD 2. MyOne Bedroom Apartment, Sleeps 3 - C$150 avg/night - Ortigia - Amenities include: Internet, Air conditioning, TV, Satellite or cable, No smoking Bedrooms: 1 Sleeps: 3 Minimum 2 night(s) stay Bookable directly online - Book vacation rental 11131246 with Vrbo. Biochemistry. ch>: > Hi Nathalie, > > It seems that CHARMM doesn't read the residue number correctly: > > 2011/6/29 Gianluca Interlandi <gianluca_at_u. com) Date: Sat Dec 04 2010 - 02:07:05 CST Next message: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Previous message: Gianluca Interlandi: "Re: Jarzinsky's equation" Next in thread: Gianluca Interlandi: "Re: Fwd:. Chemistry. Cancellation policy. com) Date: Fri Aug 30 2013 - 18:19:04 CDT Next message: Gianluca Interlandi: "Re: editing the code of the non bonded pair potentials" Previous message: Gianluca Interlandi: "Re: editing the code of the non bonded pair potentials" In reply to:. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. I made those videos seven years ago. C; the more troublesome part is the lack of long-range electrostatic treatments. washington. 7 with the PLUMED patch" Messages sorted by: [ attachment ] I found the problem. Juli 2012 00:26 > An: Aron Broom > Cc: NAMD list > Betreff: Re: namd-l: Running NAMD on Forge (CUDA) > > Yes, I was totally surprised, too. Previous message: Gianluca Interlandi: "Re: tools for Charmm" In reply to: Gianluca Interlandi: "Re: Charmm" Messages sorted by: [ attachment ] On 02/20/2014 01:10 PM, Gianluca Interlandi wrote: > I usually use the CHARMM program itself to generate a CHARMM PSF file. edu) Date: Fri May 04 2007 - 17:53:42 CDT Next message: Lechuga, Javier: "Simulating air with NAMD" Previous message: Gianluca Interlandi: "Re: query about wrapped coordinates" Maybe in reply to: Gianluca Interlandi: "Re: query about wrapped coordinates" INVENTING THE FUTURE OF MEDICINE. uiuc. edu> > wrote: > are other people also using those GPUs? > >Previous message: Gianluca Interlandi: "Conversion for forces" In reply to: Gianluca Interlandi: "Conversion for forces" Next in thread: Gianluca Interlandi: "SMD and restart" Reply: Gianluca Interlandi: "SMD and restart" Messages sorted by: [ attachment ] kcal/mol/A^2 is actually units for a force constant (for a spring for. at 298. 7 ns/day, which seems decent given the system size. edu Subject: RE: vmd-l: Can't read DCD files generated using NAMD. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"Gianluca Interlandi Foege N430E gianluca_at_uw_dot_edu. Katrina T. Fwd: Installing NAMD on windows. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. 7 with the PLUMED patch. From: Victor Kwan (vkwan8_at_uwo. Re: Does Berendsen increase viscosity of water? From: Gianluca Interlandi (gianluca_at_u. From: Buddhadev Maiti (bmaiti_at_gsu. edu) Date: Wed Sep 29 2010 - 16:34:24 CDT Next message: Gianluca Interlandi: "Re: Re: Experience with Asus Netbook" Previous message: TRINH Minh Hieu: "Re: Re: Experience with Asus Netbook" In reply to: TRINH Minh Hieu: "Re: Re: Experience with Asus Netbook" Next in. But, using the PBC my protein is continuous. On Thu, Oct 20, 2011 at 05:48:32PM -0700, Gianluca Interlandi wrote: > Dear VMD users, > > A while ago I bothered this list asking for recommendations for a > lightweight laptop to buy which would support a decent 3D acceleration in > order to use VMD in presentations. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. Department of Bioengineering, University of Washington, Seattle, Washington, 98195. Email:. Bathrooms: 1. Proteins 78, 2506–2522 [PMC free article] [Google Scholar]Previous message: Gianluca Interlandi: "Re: Compiling NAMD 2. washington. washington. Facilities. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. washington. I got 0. 1 2 3 Barry Lutz starts tenure-track position, Gianluca Interlandi joins faculty and Suzie Pun is promoted to full professor UW Bioengineering is pleased to announce. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. edu > <mailto:gianluca_at_u. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. I have a new computer that came with Windows 10, which uses UEFI with a disk that has a GPT label. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. edu>> > > I suspect that E3_19 might not be stable with this type of > implicit solvent model (it doesn't contain a term to take the > non-polar solvation energy into accout). Michel Espinoza-Fonseca: "Re: Vibrational. 7 released" Messages sorted by: [ attachment ] Thank you very much! It seems to be up to 40% faster than the 2. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. 50% refund of amount payable if you cancel at least 7 days before check-in. I was recording the energies once every 100 steps. edu] Sent: Monday, June 20, 2016 12:46 PM To: Richard Wood Cc: John Stone; vmd-l_at_ks. washington. Michel Espinoza-Fonseca: "Re: Vibrational mode analysis" In reply to: L. Usually, this > is > written in the dcd file if you specified "DCDUnitCell yes" in your > NAMD > config file. I’m working in Research Assistant Professor Gianluca Interlandi’s research lab, and I study the behavior of the Von Willebrand factor (VWF), which is a plasma protein that recruits platelets to the site of blood vessel injury. In reply to: Gianluca Interlandi: "RE: Force field design" Messages sorted by: [ attachment ] Ouch. Join Facebook to connect with Gianluca Interlandi and others you may know. washington. SASA in NAMD is used > internally to perform simulations in implicit solvent, whereas SASA in > VMD is used to analyse trajectories. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). Thanks for the reply. edu> wrote: > A few of the simulations aborted with the following message: >> "ERROR: Atoms moving too fast; simulation has become unstable. , "not. In reply to: Gianluca Interlandi: "Compiling NAMD 2. Re: Vibrational mode analysis. 7 released. 7b1 on NCSA. edu) Date: Thu Jul 16 2015 - 16:20:34 CDT Next message: Simon Kit Sang Chu: "Minimization without MD" Previous message: Gianluca Interlandi: "Re: namd ibverbs" In reply to: Gianluca Interlandi: "Re: namd ibverbs" Next in thread: Maxime Boissonneault: "Re: namd ibverbs" The bacterial adhesin FimH is a model for the study of protein allostery because its structure has been resolved in multiple configurations, including the active and the inactive state. On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi < gianluca_at_u. washington. Friend and Aachal Jalan and Shivani Gupta and Gianluca Interlandi and Yan Liu* and Veronika Tchesnokova. edu) Date: Thu Jul 16 2015 - 16:20:34 CDT Next message: Simon Kit Sang Chu: "Minimization without MD" Previous message: Gianluca Interlandi: "Re: namd ibverbs" In reply to: Gianluca Interlandi: "Re: namd ibverbs" Next in thread:. washington. Re: Help building a desktop for namd. Policies. washington. From: Gianluca Interlandi (gianluca_at_u. washington. Re: Protein in/out of box. Join Facebook to connect with Gianluca Interlandi and others you may know. washington. On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi < gianluca_at_u. Gianluca Interlandi Curriculum Vitae Department of Bioengineering, University of Washington, 1705 NE Pacific Street, 98195 Seattle, WA, [email protected]> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on small On Wed, 16 Sep 2020 at 11:40, Gianluca Interlandi <gianluca_at_u. edu) Date: Wed May 06 2009 - 11:04:21 CDT Next message: Anton Arkhipov: "Re: Langevin damping coefficient" Previous message: Benjamin Stauch: "diffusion / fex peptide problem" In reply to: Anton Arkhipov: "Re: Langevin damping. Re: external force. From: Gianluca Interlandi (gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. From: Axel Kohlmeyer (akohlmey_at_gmail. uiuc. To: Gianluca Interlandi <gianluca_at_u. 7 with the PLUMED patch" Previous message: Alex Liu: "Fix atoms-Colvars" Next in thread: Gianluca Interlandi: "Re:. One of the. -michael On Jun 15, 2006, at 5:31 PM, Gianluca Interlandi wrote:> 2011/6/29 Gianluca Interlandi <gianluca_at_u. On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. Citat Gianluca Interlandi <gianluca_at_bioc. Be the first to write a review. C; the more troublesome part is the lack of long-range electrostatic treatments. Education/training Institution and location Dates attended Degree Conferred Field of studyGianluca On Sun, 30 Aug 2009, Gianluca Interlandi wrote: > Thanks Axel, > > I have also compared the cost of a GPU equiped PC versus a dual Quadcore PC. washington. edu) Date: Thu Mar 17 2011 - 17:58:46 CDT Next message: Giacomo Fiorin: "Re: GBIS and ABF" Previous message: Branko: "GBIS and ABF" Messages sorted by: [ attachment ] Dear Jim, Do you happen to have the charmm++. 9. From: Gianluca Interlandi (gianluca_at_u. > > > > Forget about creating a pdb file. Both > simulations were started from X-ray structures. washington. edu) Date: Thu Jan 06 2011 - 16:55:03 CST Next message: Gianluca Interlandi: "Re: Compiling NAMD 2. This school has it's > own biophysics division. 26055 Abstract The blood protein von Willebrand factor (VWF) is a key link between inflammation and pathological thrombus formation. 7b1 on NCSA Abe" Next in thread: Gianluca Interlandi: "Re: Namd-I: Implicit solvent problem" Messages sorted by: [ attachment ] Hi Enrico. 0 and 2. Cheers, Johan On Thu, Apr 7, 2011 at 4:40 PM, Gianluca InterlandiReply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] So your speed for 1 or 2 GPUs (based on what your sent) is about 1. edu) Date: Tue Sep 15 2020 - 20:34:44 CDT Next message: Kodituwakku,Dimuthu Nirmani: "Re: Post processing NAMD trajectory" Previous message: Victor Zhao: "Re: Re: AMBER input and REST2 leads to crash" Next in thread:. 7b1 on Abe" In reply to: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" Messages sorted by: [ attachment ] The amount of computational work that you have for the nonbonded short-range interactions (which is the dominant part of the overallRe: Help building a desktop for namd. Sarah Keller Professor. edu) Date: Wed Sep 23 2015 - 13:37:27 CDT Next message: Gianluca Interlandi: "SSD vs SSHD vs mechanical" Previous message: Mayne, Christopher G: "Re: FFTK Bond optimization" In reply to: Gianluca Interlandi: "SSD vs SSHD vs mechanical" Next in thread: Gianluca Interlandi: "Re:. uiuc. Kitchen. ca) Date: Tue Oct 31 2023 - 20:31:14 CDT Next message: Gianluca Interlandi: "Re: VMD openGL over ssh from a server with NVIDIA" Previous message: Victor Kwan: "Re: VMD openGL over ssh from a server with NVIDIA" In reply to: Gianluca Interlandi: "Re: VMD openGL over ssh from a. com) Date: Thu Apr 05 2012 - 16:21:19 CDT Next message: Axel Kohlmeyer: "Re: DCD" Previous message: Buddhadev Maiti: "RE: DCD" In reply to: Gianluca Interlandi: "Re: DCD" Messages sorted by: [ attachment ] Hi Maiti, In TCL you can also use the 'animate' command. The structure was derived from the complex co-crystallized with botrocetin (PDB code 1U0N) (), because this is the only structure of the complex where 11 amino acids of the A1 N-terminal linker were resolved (other structures. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. washington. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"Re: Langevin damping coefficient. 1. washington. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallNext in thread: Gianluca Interlandi: "Re: NAMD 2. From: Gianluca Interlandi (gianluca_at_u. Gianluca On Sun, 30 Aug 2009, Gianluca Interlandi wrote: > Thanks Axel, > > I have also compared the cost of a GPU equiped PC versus a dual Quadcore PC. It's > slightly faster but still not that much faster than running on 16 CPU cores. washington. 1 the measure command of VMD can also > calculate the energy: > > energy energy_term atom_list [parameters] [options]: Returns the > specified energy term for a given set of atoms. edu> wrote: > Hi Fatemeh, > > Thanks for replying. Search for: Main Menu. NAMD supports CHARMM22 parameter files. edu> wrote: > Hi Fatemeh, > > Thanks for replying. In reply to: Gianluca Interlandi: "Vibrational mode analysis" Next in thread: Richard Law: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] CHARMM does normal mode. 3 hours/ns (stepsize 1, fullElectFrequency 1 and stepspercycle 20). washington. washington. e. You should simulate it in explicit water (or try one of the implicitRe: Protein in/out of box. I doubt that there is a way to haveReply: Gianluca Interlandi: "Re: NAMD timestep and numsteps" Messages sorted by: [ attachment ] Hi NAMD users, I was running a simulation using NAMD with timestep 5 fs and numsteps 5000. The energy term mustOn Mon, 11 Apr 2011, Gianluca Interlandi wrote: > Salvador, > > You might also want to apply for computing time at one of the national > supercomputing centers through Teragrid. VMD-L Mailing List. edu) Date: Wed Oct 20 2010 - 15:33:33 CDT Next message: jnsong: "how to cenvert NAMD binary coordinate file to text file" Previous message: Jim Phillips: "Re: NAMD 2. (did you see if any hunk failed?) Gianluca > Gianluca > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? I wonder if the prebuilt > smp one is just not > working for you. edu > Betreff: Re: namd-l: Mysterious slow down in parallel > > You should read about domain decomposition. edu> wrote:Next in thread: Gianluca Interlandi: "Re: Infiniband and PME gridsize" Reply: Gianluca Interlandi: "Re: Infiniband and PME gridsize" Messages sorted by: [ attachment ] I don't think we have ever run NAMD on infiniband. The Bacterial Fimbrial Tip Acts as a Mechanical Force Sensor. My> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. Re: Langevin process in NAMD tutorial"Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. >> >> According to your banchmarks, it looks like the less expensive GTX285 >> (around 300$) performs better than a Tesla C1060 which is 4 times more >> expensive. 1002/prot. Kisiela, # 1 , * Hovhannes Avagyan, # 1 Della Friend, 2 Aachal Jalan, 1 Shivani Gupta, 3 Gianluca Interlandi, 3 Yan Liu, 4 Veronika Tchesnokova, 1 Victoria. Neil King Assistant Professor. RE: Force field design. washington. edu> wrote: In reply to: Gianluca Interlandi: "Compiling NAMD 2. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of HealthRe: NAMD 2. washington. washington. 0 and 2. running multicore version on a 2-CPU node. 10. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). From: Gianluca Interlandi (gianluca_at_u. 97 pN*nm = 1 Kcal/molIn reply to: Gianluca Interlandi: "RE: Force field design" Messages sorted by: [ attachment ] Ouch. RE: Force field design. Michel Espinoza-Fonseca: "Re: Vibrational. , and Thomas W. From: Gianluca Interlandi (gianluca_at_u. Living Room. View the profiles of professionals named "Gianluca Interlandi" on LinkedIn. uiuc. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. washington. What can be the possible cause for this or does it happens naturallyOn Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. washington. washington. Just a good MD toy ! Victor owner-namd-l_at_ks. I would be > happy if somebody could point me out to some scripts which help me perform Hemostasis in vertebrates involves both a cellular and a protein component and von Willebrand factor evolved in the ancestral vertebrate following the divergence of the urochordates some 500 million years ago and that it acquired increasing complexity though sequential insertion of functional modules. 6 version, although I am not running the cluster at full load yet. 15 K 1 KT = 2. >From: Gianluca Interlandi (gianluca_at_u. uiuc. Gianluca Interlandi, Department of Bioengineering, University of Washington, Box 355061, 3720 15th Ave NE, Seattle, WA 98195-5061, USA. edu] > Sent: Thursday, April 05, 2012 5:04 PM > To: Buddhadev Maiti > Cc: Jérôme Hénin; namd-l_at_ks. On 6 May 2009, at 11:04, Gianluca Interlandi wrote: > Thanks Anton for your answer. From: Mitchell Gleed (aliigleed16_at_gmail. washington. washington. edu) Date: Wed May 06 2009 - 11:04:21 CDT Next message: Anton Arkhipov: "Re: Langevin damping coefficient" Previous message: Benjamin Stauch: "diffusion / fex peptide problem" In reply to: Anton Arkhipov: "Re: Langevin damping coefficient" Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build?On Mon, Aug 26, 2013 at 12:56 PM, Gianluca Interlandi < gianluca_at_u. washington. Chemistry. I would be > happy if somebody could point me out to some scripts which help me perform(no subject) From: BIPLAB NANDI (dafodils2002_at_gmail. We are building a smaller cluster though in the lab and will test the scalabilityGianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. washington. VMD-L Mailing List. E-mail: [email protected] > Betreff: Re: namd-l: Mysterious slow down in parallel > > You should read about domain decomposition. If I > want to use all 6 CUDA devices in a node, how many processes is it > recommended to spawn?> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. edu > Betreff: Re: namd-l: Mysterious slow down in parallel > > You should read about domain decomposition. It's > slightly faster but still not that much faster than running on 16 CPU cores. Semantic Scholar's Logo. washington. > > Forget about creating a pdb file. edu> wrote: > Dear all, > > Does anybody have any recommendation how to convert a solvated system > (protein + solvent + ions) PDB + PSF from the CHARMM to the Amber force > field so that it can be used in NAMD with the. From: Ernesto Vargas (vargaslo_at_gmail. Reply: Gianluca Interlandi: ""wrapAll on" with a complex" Reply: Gianluca Interlandi: "Scale" Messages sorted by: [ attachment ] Dear NAMD users, I'm performing SMD simulations and I have problems when I restart a simulation, i. Managing Member/Principal Atlantic Mortgage Partners, LLC Jun 2009 - Jun 2012 3 years 1. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. edu) Date: Mon Oct 11 2010 - 16:56:03 CDT Next message: Basak Isin: "Re: Regarding answering questions in a forum. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. Gianluca, Looking at the code, it does not, but that would be easy to adapt from the NAMD's ComputeCrossterms. 7 with the PLUMED patch" In reply to: Gianluca Interlandi: "Compiling NAMD 2. washington. , heavy winds caused a tree along the Burke-Gilman Trail to break in half, nearly striking a cyclist and pedestrians. Gianluca On Thu, 6 Jan 2011, Gianluca Interlandi wrote: > Hi!Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit : > I am performing a simulation of a complex consisting of two proteins. I'm testing specifically this protein for its beaviour. Previous message: Gianluca Interlandi: "stepspercycle" In reply to: Gianluca Interlandi: "stepspercycle" Next in thread: Gianluca Interlandi: "Re: AW: stepspercycle" Reply: Gianluca Interlandi: "Re: AW: stepspercycle" Messages sorted by: [ attachment ] No idea where you were looking, but this parameter is still fundamental for. washington. From: Gianluca Interlandi (gianluca_at_u. 7 released" Messages sorted by: [ attachment ] Hi all, I pushed 2. washington. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallYesterday at about 11:45 a. Entertainment. I > attach a plot of a constant velocity simulation where I'm pulling two > proteins apart. Gianluca Interlandi [email protected] orcid. uiuc. There are 3 professionals named "Gianluca Interlandi", who use LinkedIn to exchange. From: Gianluca Interlandi (gianluca_at_u. Name : Current Position : Tim Connolley, Bioengineering 2005 : Michigan State Mechanical Engineering Graduate Program: Brett Anderson, Bioengineering 2006Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of HealthCorrespondence to: Gianluca Interlandi, Department of Bioengineering, University of Washington Box 355061, 3720 15th Ave NE, Seattle, WA 98195-5061, USA. 7 released" Messages sorted by: [ attachment ] Dear Jim, Do you happen to have the. Previous message: Gianluca Interlandi: "NAMD 2. edu> > wrote: > Roy, > > I think that you are confusing two things.