Re: [gmx-users] is there a way to get pullx.xvg and pullf.xvg from traj_comp.xtc?

Thanks Justin, mdrun -rerun works. But I failed to fix it via gmx traj with this command: gmx traj -f traj_comp.xtc -s topol.tpr -ox pullfx.xvg -of pullf.xvg -dt 400 error say .xtc file do not have force information. Is the command I used correct? -- Gromacs Users mailing list * Please search

Re: [gmx-users] md with multiple ligands

Well it depends how the OP has set up their simulation. Was trying to help. :) What you're saying is right of course. On 2 July 2016 at 21:45, Justin Lemkul wrote: > > > On 7/1/16 9:51 PM, Billy Williams-Noonan wrote: > >> Hi Justin, >> >> I've found that I get this error

Re: [gmx-users] Fwd: Problem in applying walls in the z direction

I notice that they are the hydrogen atoms of the same water molecule and they may have been split by the PBC in the previous step. I'll prepare the gro again. Thanks for your help. Cheers On 07/02/16 22:23, Justin Lemkul wrote: On 7/2/16 4:20 PM, Stephen Chan wrote: Hi Justin, Just above

Re: [gmx-users] Fwd: Problem in applying walls in the z direction

On 7/2/16 4:20 PM, Stephen Chan wrote: Hi Justin, Just above the fatal error message, there is some additional information: Initializing Domain Decomposition on 112 ranks Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter

Re: [gmx-users] Fwd: Problem in applying walls in the z direction

Hi Justin, Just above the fatal error message, there is some additional information: Initializing Domain Decomposition on 112 ranks Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded

Re: [gmx-users] Fwd: Problem in applying walls in the z direction

On 7/2/16 3:50 PM, Stephen Chan wrote: Dear all, I'm running a simulation of a bilayer system and I would like to apply wall condition to both xy planes (i.e. nwall = 2). On top of the normal MD settings, I added a couple of lines to the mdp file: pbc = xy nwall = 2

[gmx-users] Fwd: Problem in applying walls in the z direction

Dear all, I'm running a simulation of a bilayer system and I would like to apply wall condition to both xy planes (i.e. nwall = 2). On top of the normal MD settings, I added a couple of lines to the mdp file: pbc = xy nwall = 2 wall-type = 10-4 wall-density= 5

Re: [gmx-users] protein has broken after 100ns simulation

Have you tried pbc nojump or whole with trjconv? Sent from my iPhone > On 02-Jul-2016, at 11:46 am, Seera Suryanarayana wrote: > > Dear gromacs users, > > I have simulated protein for 100ns. When I visualized the protein in VMD, I > have seen the protein into different

Re: [gmx-users] g_mmpbsa python script error

On 7/2/16 9:22 AM, Amali Guruge wrote: Dear All, I installed g_mmpbsa tool for binding energy calculation for my GROMACS runs. When I gave the command, python MmPbSaStat.py -m energy_MM.xvg -p polar.xvg -a sasa.xvg I got the following error. python: can't open file 'MmPbSaStat.py': [Errno

[gmx-users] g_mmpbsa python script error

Dear All, I installed g_mmpbsa tool for binding energy calculation for my GROMACS runs. When I gave the command, python MmPbSaStat.py -m energy_MM.xvg -p polar.xvg -a sasa.xvg I got the following error. python: can't open file 'MmPbSaStat.py': [Errno 2] No such file or directory Please can

Re: [gmx-users] charge assign

On 7/2/16 2:37 AM, elham tazikeh wrote: Dear Justin i really appreciate for your reply i think my question wasn't clear. i prefer to express my problem again: i'd like to accomplish protein-drug simulation by gromos force field and before, docked my ligand on the protein (because,there wasn't

[gmx-users] Issue with number of cores

Dear Gromacs users I want to do a mdrun on my system which has 7 cores but I just want to use 5 of them. Is there anyway to use 5 of them without effecting on the remained ones ? I have used the remained ones with another software before. I really appreciate it if� you can

Re: [gmx-users] md with multiple ligands

On 7/1/16 9:51 PM, Billy Williams-Noonan wrote: Hi Justin, I've found that I get this error with my relative FEP calculations if my .gro file with the relevant protein and ligand coordinates, describes the protein numbering from a1-3017, and the ligand from 3018 onwards for example, while in

Re: [gmx-users] is there a way to get pullx.xvg and pullf.xvg from traj_comp.xtc?

On 7/1/16 6:28 PM, Ming Tang wrote: Dear list, I did SMD, but saved the pullx.xvg and pullf.xvg much less frequently compared to the traj_comp.xtc. is it possible to get a more frequently written pull COM coordinates and forces based on the traj_compxtc file I have? Either use mdrun

Re: [gmx-users] No velocity and transitional kinetic energy calculated from gmx traj

On 7/1/16 4:43 AM, Bui, Tai wrote: Dear Gromacs users, I want to calculate velocity and transitional kinetic energy of one molecule (CH4 united atom) during the simulation. I tried to use gmx traj, however it gave me 2 output files without any results for the velocity and the energy I

Re: [gmx-users] protein has broken after 100ns simulation

Hi, The mailing list removes attachments. Your best bet is uploading your snapshot to an image sharing service. Sometimes several uses of trjconv are required to fix pbc issues. > On 02 Jul 2016, at 08:16, Seera Suryanarayana wrote: > > Dear gromacs users, > > I have

[gmx-users] No velocity and transitional kinetic energy calculated from gmx traj

Dear Gromacs users, I want to calculate velocity and transitional kinetic energy of one molecule (CH4 united atom) during the simulation. I tried to use gmx traj, however it gave me 2 output files without any results for the velocity and the energy I wanted. The command I did is: gmx traj -f

[gmx-users] charge assign

Dear Justin i really appreciate for your reply i think my question wasn't clear. i prefer to express my problem again: i'd like to accomplish protein-drug simulation by gromos force field and before, docked my ligand on the protein (because,there wasn't the crystallography file of this complex).

[gmx-users] protein has broken after 100ns simulation

Dear gromacs users, I have simulated protein for 100ns. When I visualized the protein in VMD, I have seen the protein into different fragments. Later I came to know that there is no breaking phenomena in simulations and that is because of the PBC problems. I have executed the trjconv command with