Re: [gmx-users] gromacs 5.1.2 MPI performance

Can you tell everyone your system size? 112 cores could be 7 X 16 or 14 X 8, which is indeed weird. Have you tried 4 X 8, 6 X 8, or 12 X 8? These look more natural to me. On Thu, Sep 8, 2016 at 9:08 PM, Stephen Chan wrote: > Hello, > > I am compiling an MPI version

[gmx-users] Simulated tempering in gromacs

Dear List, I'd like to use "simulated tempering" to increase my sampling efficiency as I am trying to fold a polymer from its extended conformation. I understand that GROMACS 5 can easily handle replica-exchange MD, but my system is too large (>100K atoms) and there would be too many replicas...

[gmx-users] vdw-type and DispCorr

Hello everyone, Should DispCorr be turned off if I am using vdw-type = PME (since PME already accounts for long range vdw interactions)? Also I am curious if this vdw PME option is designed to suit some specific force fields? Thanks for any thoughts. Yun -- Gromacs Users mailing list *

[gmx-users] Empty output files from gmx helix?

Hi everyone, I have a 21-mer peptide A for helix analysis using gmx helix in GROMACS 5. When I select residues 3-19 when executing gmx helix, everything looks fine. But when I select another set of residues, e.g. 8-19, the output len-ahx.xvg file ends after: # This file was created Thu Jun 9

Re: [gmx-users] updates about ACPYPE

Hi Alan, Is this Rev: 403? And does the --gmx45 still compatible with gromacs5 (although gromacs says its version 5 is mostly backward compatible with version 4)? On Sat, Aug 30, 2014 at 8:40 PM, Alan wrote: > Dear community, > > Many thinks for all of you who uses ACPYPE

Re: [gmx-users] First frame already out of box, getting very large RMSD

On Sun, Mar 1, 2015 at 5:42 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/1/15 8:26 PM, yunshi11 . wrote: On Sun, Mar 1, 2015 at 4:36 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/1/15 3:47 PM, yunshi11 . wrote: On Sun, Mar 1, 2015 at 11:43 AM, Justin Lemkul jalem...@vt.edu wrote

Re: [gmx-users] First frame already out of box, getting very large RMSD

On Sun, Mar 1, 2015 at 4:36 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/1/15 3:47 PM, yunshi11 . wrote: On Sun, Mar 1, 2015 at 11:43 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/1/15 1:21 PM, yunshi11 . wrote: On Sat, Feb 28, 2015 at 4:40 PM, Justin Lemkul jalem...@vt.edu wrote

Re: [gmx-users] First frame already out of box, getting very large RMSD

On Sat, Feb 28, 2015 at 4:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/28/15 7:38 PM, yunshi11 . wrote: On Sat, Feb 28, 2015 at 4:21 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/28/15 7:17 PM, yunshi11 . wrote: On Sat, Feb 28, 2015 at 3:03 PM, Justin Lemkul jalem...@vt.edu wrote

Re: [gmx-users] First frame already out of box, getting very large RMSD

On Sun, Mar 1, 2015 at 11:43 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/1/15 1:21 PM, yunshi11 . wrote: On Sat, Feb 28, 2015 at 4:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/28/15 7:38 PM, yunshi11 . wrote: On Sat, Feb 28, 2015 at 4:21 PM, Justin Lemkul jalem...@vt.edu wrote

Re: [gmx-users] First frame already out of box, getting very large RMSD

On Sat, Feb 28, 2015 at 3:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/28/15 6:00 PM, yunshi11 . wrote: Dear all, I am running MD for a protein-ligand complex in a dodecahedron box and followed the Suggested trjconv workflow from http://www.gromacs.org/Documentation/Terminology

[gmx-users] First frame already out of box, getting very large RMSD

Dear all, I am running MD for a protein-ligand complex in a dodecahedron box and followed the Suggested trjconv workflow from http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions . Now I wonder how to remove jumps (across periodic boxes) when the first frame (actually

Re: [gmx-users] First frame already out of box, getting very large RMSD

On Sat, Feb 28, 2015 at 4:21 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/28/15 7:17 PM, yunshi11 . wrote: On Sat, Feb 28, 2015 at 3:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/28/15 6:00 PM, yunshi11 . wrote: Dear all, I am running MD for a protein-ligand complex

[gmx-users] Broken molecule across periodic boundary: The sum of the two largest charge group radii (xxx) is larger than rlist (xxx)

Hi there, I understand this is an old issue, but no one seems to have a solution? So I want to take a snapshot from the middle of a MD trajectory (like 67ns point from a 100ns trajectory), preferably with all solvent molecules (waters and ions). However, after using trjconv -pbc to make

Re: [gmx-users] Shifting in Verlet cut-off schemes?

On Mon, Mar 4, 2013 at 3:22 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Sat, Mar 2, 2013 at 6:40 PM, Yun Shi yunsh...@gmail.com wrote: Hi all, I have read http://www.gromacs.org/Documentation/Cut-off_schemes, but still unsure about how Verlet works. The group cut-off scheme

[gmx-users] Different optimal pme grid ... coulomb cutoff values from identical input files

Hello all, I am doing a production MD run of a protein-ligand complex in explicit water with GROMACS4.6.5 However, I got different coulomb cutoff values as shown in the output log files. 1st one:

[gmx-users] Since nstlist has no effect on the accuracy

In a MD run with Verlet cutoff scheme, can I set nstlist as large as possible? Like 100 or 1000? Thanks, Yun -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] z always small for domain decomposition grid?

Hi everyone, For my MD simulations on different number of CPUs (sometimes with GPUs), the domain decomposition grid that I got from automatic (not setting -dd) domain decomposition is always like: .. Domain decomposition grid 8 x 6 x 2, separate PME nodes 48 PME domain decomposition: 8 x 6 x

Re: [gmx-users] How to find the mutation effect?

What exactly is the mutation? Length of the MD run? Have you tried clustering and compare the clustered structure? On Sun, Dec 15, 2013 at 10:42 AM, xiao helitr...@126.com wrote: Dear all, I am doing a MD on a mutant protein which is unstable from exprient. However, i found no difference

[gmx-users] 3 GPUs much faster than 2 GPUs with GROMACS-4.6.2 ???

Hi all, I have a physical compute node with 2x 6-core Intel E5649 processors + three NVIDIA Tesla M2070s GPUs. First I tried using all 12 CPU cores + 3 GPUs for an equilibration run (of protein in TIP3 waters), which gave me 8.964 ns/day performance. But I noticed the PME mesh calculation,

Re: [gmx-users] load imbalance in multiple GPU simulations

. small system), even using only two of the three GPUs could improve performance Cheers, -- Szilárd On Sun, Dec 8, 2013 at 8:10 PM, yunshi11 . yunsh...@gmail.com wrote: Hi all, My conventional MD run (equilibration) of a protein in TIP3 water had the Average load imbalance: 59.4 % when