[gmx-users] Strange self-coefficient data with "-update gpu" option

Hey, We ran a quick simulation of a box of 884 spce water model using Gromacs 2020 on a workstation with an RTX 2080 card. The water box was generated using gmx solvate command. The whole simulation is 10 ns NPT + 10 ns NVT. The self-diffusion coefficient is D[OW] = 23.5350 (+/- 11.1866)

Re: [gmx-users] Regarding high RMSD

Thank for your suggestion Alessandra I have applied the pbc conditions on my system in steps as follows: 1. gmx trjconv -f full_md.xtc -s full_md.tpr -pbc whole -o full_md_whole.xtc 2. gmx trjconv -f full_md_whole.xtc -s first_frame.gro -pbc nojump -o full_md_nojump.xtc 3. gmx trjconv -f

[gmx-users] Residue-Specific CMAPS in GROMACS

Hi all, I've been investigating the implementation of CMAP in GROMACS and, as far as I understood, the current CMAP format does not allow the use of residue-specific CMAPS, since it is based on atomtypes and not on function numbers, as GROMACS normally do. For example, for AMBER, the function

Re: [gmx-users] Troubleshooting Error Message: Invalid Index Group References

Thanks for your response! I checked and the cg_traj file contains atoms numbered 1-2000, which matches the atom IDs from the index file. The same trajectory does work using gmx angle with an angle index file created from the same python script which also includes atom IDs 1-2000 as well.

Re: [gmx-users] gmx_topolbuild error (aayatt...@bose.res.in)

On Fri, 10 Jan 2020 11:15:36 +0530 (IST) , aayatt...@bose.res.in wrote: Date: Fri, 10 Jan 2020 11:15:36 +0530 (IST) From: aayatt...@bose.res.in To:

Re: [gmx-users] pdb2gmx picks up the wrong .tdb files?

On 1/17/20 4:25 AM, András Ferenc WACHA wrote: Dear Justin, there are no name clashes in the .rtp files by design, I never re-use already existing residue names. Beta3-homo-lysine is B3K, beta2-homo-lysine is B2K, and disubstituted amino-acids also have their naming scheme. Sorry, no idea.

Re: [gmx-users] com motion and position restraints may cause artifacts

On 1/17/20 3:01 AM, Berk Hess wrote: Hi, Using center of mass motion removal in combination with an absolute reference in the system, such as position restraints, will always lead to artifacts, as physical motion is removed and not drift due to numerical rounding errors. For the most

Re: [gmx-users] Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?

On 1/17/20 7:12 AM, ZHANG Cheng wrote: Many thanks for Justin's advice forassigning the same number of PP and PME ranks in each run (30/6 in 5.1.1 and 27/9 in 2019.3). Sorry I am not familiar with these kind of settings, can I ask how to do this exactly? e.g. how to change "gmx mdrun

Re: [gmx-users] Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?

Many thanks for Justin's advice forassigning the same number of PP and PME ranks in each run (30/6 in 5.1.1 and 27/9 in 2019.3). Sorry I am not familiar with these kind of settings, can I ask how to do this exactly? e.g. how to change "gmx mdrun -deffnm md_0_1 -cpi -append" ?

Re: [gmx-users] Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?

He said he ran a nearly identical simulation on two versions of gromacs but I didn't think so, in 2019.3 logs: There are: 117860 Atoms Atom distribution over 27 domains: av 4365 stddev 75 min 4289 max 4626 and 5.1 logs: There are: 127790 Atoms Atom distribution over 30 domains: av 4259 stddev 90

[gmx-users] Ran into trouble installing Gromacs API

Hello I have (I think successfully) installed Gromacs 2020 on my computer (MacOS X Catalina) and tried to install the API using the quick install guide: https://gmxapi.readthedocs.io/en/latest/quickstart.html and get stuck on the step: pip install -r requirements.txt as that file does not

Re: [gmx-users] pdb2gmx picks up the wrong .tdb files?

Dear Justin, there are no name clashes in the .rtp files by design, I never re-use already existing residue names. Beta3-homo-lysine is B3K, beta2-homo-lysine is B2K, and disubstituted amino-acids also have their naming scheme. Andras On 1/16/20 11:34 PM, Justin Lemkul wrote: > > > On 1/16/20

Re: [gmx-users] cluster analysis_group selection

Hi, Hope this helps: https://ctlee.github.io/BioChemCoRe-2018/clustering/ In case you may want to align the trajectory using one group but calculate RMSD using another group, you can choose no fit when doing clustering. In that case, gmx trajconv can be used before doing clustering. Best, Jin --

Re: [gmx-users] Problem while running equilibration

Hi, see some comments/suggestions below. Best regards Alessandra On Fri, Jan 17, 2020 at 8:34 AM Nirali Desai wrote: > Dear all, > > My system consists of a three chains of protein: PROA, PROB and PROCLIG > (with ligand). > Minimization is running properly without any error. > Parameters used

Re: [gmx-users] Regarding high RMSD

Hi, On Fri, Jan 17, 2020 at 6:39 AM Ashma Khan wrote: > Thank you for your suggestion Alessandra Villa > I have applied all types of pbc conditions but my one peptide is diffusing > away from another peptide in case of dimer after half of the simulation > time and rmsd is coming out 100

Re: [gmx-users] com motion and position restraints may cause artifacts

Hi, Using center of mass motion removal in combination with an absolute reference in the system, such as position restraints, will always lead to artifacts, as physical motion is removed and not drift due to numerical rounding errors. For the most common case of equilibrating macromolecules