[gmx-users] position restraints on backbone: index error

Dear Gromacs users, I would like to run protein/protein interaction simulation (consisting of 5 chains) that holds the backbone atoms rigid but allows side-chain movements. According to the Gromacs documentation this should work by: "Special position restraint .itp files can be created using the

Re: [gmx-users] position restraints on backbone: index error

Hi, Position restraints are per molecule. if you separate your molecule like that, the position restraints of backbone should be generated for each chain base on indices of each chain and include it in the topology of the chain, not global topology like that. so for example, if you want restraint

Re: [gmx-users] Fwd: Probability of number of atomic contacts

Hi Mark, Thank you for your reply! Actually, I should clarify my last post because it seems that I repeated my question :-) When I use the tool that Justin suggested, gmx analyze -dist, on the generated file from gmx mindist for the number of contact, I can get the probability of number of

Re: [gmx-users] edit dhdl.xvg file

On 3/1/19 2:38 PM, Qasim Pars wrote: Dear users, I am trying to edit the dhdl.xvg files obtained from free energy calculation but couldn't do it. For instance, is that possible to delete the last 5 ns from the dhdl.xvg file including the data of 25 ns by using one of GROMACS tools? If yes,

Re: [gmx-users] edit dhdl.xvg file

On 3/1/19 2:43 PM, Qasim Pars wrote: No, I won't use gmx bar. It's trivial to delete lines using a text editor, but always keep a backup, or otherwise instruct whatever analysis program you're using to consider only the range of time you want, as GROMACS would do with -b and -e.

[gmx-users] edit dhdl.xvg file

Dear users, I am trying to edit the dhdl.xvg files obtained from free energy calculation but couldn't do it. For instance, is that possible to delete the last 5 ns from the dhdl.xvg file including the data of 25 ns by using one of GROMACS tools? If yes, which tool can do this? Thanks in advance.

Re: [gmx-users] Pulling ion across the bilayer-choosing pull_coord1_geometry

On 2/28/19 2:09 PM, Javad Deylami wrote: Hi Justin, I have one general and one specific question about doing the pulling simulation. Can you let me know how I should choose pull_coord1_geometry among distance, direction, and cylinder? How can I distinguish these three geometries to use them

[gmx-users] Output files RMSD (xvg). Convert Nanometer to Angstrom.

Dear, There is some command to convert my output files from the molecular dynamics, so that I can visualize the deviation of the trajectories in Angstroms instead of nanometers. Respectfully. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Output files RMSD (xvg). Convert Nanometer to Angstrom.

On 3/1/19 8:28 AM, Edjan Silva wrote: Dear, There is some command to convert my output files from the molecular dynamics, so that I can visualize the deviation of the trajectories in Angstroms instead of nanometers. GROMACS uses SI units for everything. It is simple to write a script that