Re: [gmx-users] Response required

Hi, I suggest you explore the LigParGen software for its documentation and help fora. This one is particular to GROMACS. Mark On Fri, Dec 28, 2018 at 3:50 PM wrote: > > Hi everyone > > When I submit a PEO chain consists of 23 monomers to LigParGen > web-based service to make a topology file,

Re: [gmx-users] how to calculated potential energy ?

Hi, You can use trjconv and tpbconv to make matching subsets of the trajectory and tpr files, and then mdrun -rerun will compute the contributions on those subsets. But I doubt there's force fields where any of this is meaningful. Mark On Tue, Jan 1, 2019 at 1:47 PM milad bagheri wrote: > Dear

Re: [gmx-users] AMD 32 core TR

Hi, Thanks for the report. Glad to hear things work well when you use matching stuff, and particularly the latest stuff. Note that adding more CPU cores will only help throughput if there is significant remaining workload on the CPU. There is advice at the bottom of the log file in cases where th

[gmx-users] Box gets big when using walls during NPT

Hello GMX users, The initial size of the simulation box is 8x8x8. I need to use walls during NPT production, thus I set up this ewald-geometry = 3dc nwall = 2 wall-atomtype = opls_097 opls_097 wall-type= 12-6 wall-r-linpot = -1 wall-ewa

Re: [gmx-users] AMD 32 core TR

Tamas, thanks for the response. In previous posts I mention using a single gtx 1080ti, sorry for not making it clear in the last post. On the 8 core AMD and an Intel 6 core I am running Cuda 10 with Gromacs 18.3 with no issues. I believe the larger factor in the slowness of the 32 core was

Re: [gmx-users] Large system

Sir I have done a simulation of 106000 atoms and there was no problem. Check your number of molecules in your topology and inspect your input file you will find something wrong. The error says the number of atoms is not the same in topology and your input. I suggest using *.gro rather than pdb whi

Re: [gmx-users] AMD 32 core TR

Please provide more information. If you use gmx 2018 then I think that gmx limits the gcc version to 6 and not cuda 10. You did not specify what type of and how many GPUs you use. In addition, the choice of gmx for distributing computation could be also informative - you find this info in th

Re: [gmx-users] about 165 gromacs bug in the list

Den 2019-01-03 kl. 18:03, skrev Santosh Kumar Meena: Dear all, I would like to ask whether 165 gromacs bug in gromacs bug list related to non zero center of mass drift in Gromacs that became apparent only at long timescales is resolved in new versions. Thanks in advance. Regards Not that I k

[gmx-users] AMD 32 core TR

Dear users, I had trouble getting suitable performance from an AMD 32 core TR. By updating all the cuda drivers and runtime to v10 and using gcc,g++ -6 from v5 -- I did try gcc-7 but Cuda 10 did not appreciate the attempt -- and in particular removing CUDA v7 runtime.), I was able to imp

[gmx-users] about 165 gromacs bug in the list

Dear all, I would like to ask whether 165 gromacs bug in gromacs bug list related to non zero center of mass drift in Gromacs that became apparent only at long timescales is resolved in new versions. Thanks in advance. Regards -- Dr. Santosh Kumar Research Associate Department of Materials Sci

[gmx-users] Simulation with vacuum interface

Dear GMX user, I have a system box with half liquid molecules and half vacuum(vacuum on the z-direction), I want to apply an NPT simulation to study the behavior on the liquid-vacuum interface. Normally the box will just shrink to fit the liquid. Is there a way to apply NPT on the system while mai