[gmx-users] Restraints not working during minimization

> > Hi, What minimization type are you using? Quasi-Newtonian (L-BFGS) doesn’t > respect restraints; others do. Sincerely, James Ryley > > > -- > > Message: 4 > Date: Thu, 7 Feb 2019 11:03:50 +0530 > From: Ashraya Ravikumar > To:

[gmx-users] Position restrained energy minimization

Hi, I am trying to do position restrained energy minimization of a solvated peptide, where the peptide is restrained but the solvent is free to move. But I do see the positions of the atoms of the peptide change. I increased the force value in position restraint file to 1 from 1000, but it

[gmx-users] Position restrained energy minimization

Hi, I am trying to do position restrained energy minimization of a solvated peptide, where the peptide is restrained but the solvent is free to move. But I do see the positions of the atoms of the peptide change. I increased the force value in position restraint file to 1 from 1000, but it

Re: [gmx-users] g_msd Time Unit

Extremely helpful! Thanks On Wed, Feb 6, 2019 at 3:29 AM Fotis Baltoumas wrote: > Hello Tim, > > In GROMACS trajectories, the simulation time is normally saved alongside > the coordinates in the trr and xtc files as produced by GROMACS itself. > That's how the various analysis tools can

[gmx-users] Ionic conductivity

Hi thereWhen the ionic conductivity changes during the time!Analysis shows that at different time intervals, the ionic conductivity changes.I divide the production run time to 3 intervals of time. At each of them, I get a different ionic conductivity.What should I do?Thank you -- Gromacs Users

Re: [gmx-users] gmx trjconv -center not working?

Hi, There are a few issues related to gmx trjconv -center: a) http://redmine.gromacs.org/projects/redmine-platform/search?all_words=1=0=Submit=1=0=1=-center=all_only==%E2%9C%93 b) http://redmine.gromacs.org/issues/2579 but not sure if the exactly match what you have. Benson On 2/6/19 7:39

Re: [gmx-users] gmx trjconv -center not working?

...and as a follow up, it doesn't seem to be centering at either the geometric center OR the center of mass. Any insight would be appreciated. Mala On Wed, Feb 6, 2019 at 10:15 AM Mala L Radhakrishnan wrote: > Hi, > > It would be helpful to know if this is a known bug/issue. I'd rather not >

[gmx-users] Distance COM of two systems

Hello, I would like to calculate the distance from the center of masses (COM) between two systems. One would be the center of mass of waters and another would be the center of mass of a lipid membrane. I was using this command and wanted to know if it is correct. gmx pairdist -f total.xtc -s

Re: [gmx-users] gmx trjconv -center not working?

Hi, It would be helpful to know if this is a known bug/issue. I'd rather not have to write code to recenter in this case -- would be easy if I just had one molecule far from the edges of the box but I am simulating a crowded system and need to get it centered on one complex within the system

Re: [gmx-users] offloading PME to GPUs

Hi, Your log file will definitely tell you whether PME was offloaded. The performance gains depend on your hardware, particularly the CPU/GPU balance. There have been a number of threads on this forum discussing this topic, if you search back through the gmx_user archives. The gist of it is that

Re: [gmx-users] CHARMM or AMBETR forcefield for methylated glutamine and glutamic acid.

Hi, I think you should be able to do that if there are (and I think there should be) corresponding entries in the chramm/amber rtp file. If this sounds alien to you, try find out what is the way to generate topologies from a residue database (e.g. gromacs manual or tutorials). Hope this sounds

Re: [gmx-users] gmx trjconv -center not working?

Hi, I also had that experience with trjconv with various versions. I ended up doing the centering by a script. I know on the other hand that centering works well in the case of for example gmx density. Yet I've had no luck with trjconv... Maybe this is known issue..? Regards, Gyorgy On Tue, 5

[gmx-users] offloading PME to GPUs

Hello, I understood from the documentation: http://manual.gromacs.org/documentation/2018-current/user-guide/mdrun-performance.html that PME can be now offloaded to GPUs in v2018. I'm using SLURM in a machine with 24 cores, I wonder if the following script would be able to offload PME to GPUs

Re: [gmx-users] slow gmx

Hi, For use on a single workstation, rely on the built-in thread-MPI. Your library MPI system is clearly configured to expect various devices and that is slow. See e.g. http://manual.gromacs.org/documentation/current/install-guide/index.html#mpi-support And only gmx mdrun makes any use of any

[gmx-users] CHARMM or AMBETR forcefield for methylated glutamine and glutamic acid.

Dear all, I want to do the MD simulation of a protein with methylated glutamine and glutamic acid using CHARMM force field in GROMACS. Is it possible to get the GROMACS supported topology file and the parameters for CHARMM or AMBETR forcefield for methylated glutamine and glutamic acid. --

[gmx-users] slow gmx

Hello, I've installed Gromacs 2018v4 in my Linux X64 OS. When I try to run command line: gmx_mpi -h or gmx_mpi pdb2gmx -f input.pdb -o gmx.gro it is very slow. I always obtained the following information: localhost.14713hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after

[gmx-users] friction constant for free energy calculation

Dear gmx users, I was trying to calculate free energy. I’m confused about setting the appropriate value for friction constant (= 1/tau-t). In gmx manual, a value of 0.5 ps-1 (tau-t = 2.0 ps) was suggested but 1.0 ps-1 (tau-t = 1.0 ps) was used in Justin’s tutorial. How much the results are

Re: [gmx-users] g_msd Time Unit

Hello Tim, In GROMACS trajectories, the simulation time is normally saved alongside the coordinates in the trr and xtc files as produced by GROMACS itself. That's how the various analysis tools can understand time when it is required. However, NAMD does not save the simulation file in the

[gmx-users] TCAF

Hi, I have a system with an applied electric filed in x direction. I need to calculate viscosity in x direction too. How can I obtain viscosity in x direction using Tcaf? appreciate the reply, -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Domain decomposition fatal error during production run

Dear gromacs users, I performed a MD simulation on a dimer system with pulling code during the production run to force the two monomers to get closer. After 55 ns of production run I got this error : *step 30616369: Water molecule starting at atom 30591 can not be settled.Check