[gmx-users] 5. Re: 3. Re: Strange pullx coordinates (PMF calculations)

Hello Justin- In MY pullx first column is Time and second column is absolute coordinate of the COM of the pulled group Maybe we are missing an option which would print X and dX in the pullx files - one of the pull-print stuffs ???!!.. In that case too bad we would have tons of "bad" pull files

[gmx-users] Issues with specbond.dat for a HEME protein

Dear all, I'm currently trying to simulate a Cytochrome P450 protein in solution and am having trouble getting the system to give a cysteine molecule correct partial charges in Gromacs 2018.1. In my system the CYS400 residue should ligate to the HEM(471) motif and, from the PDB file, I have

Re: [gmx-users] Regarding xpm2ps with a xpm file obtained from gmx densmap [update] and possible bug

Hello again, Does the GROMACS team have some suggestions to help me to resolve my problem with the output of gmx densmap and xpm2ps to an eps/pdf with all the ticks in the x/y axis (see below)? Since it seems a small bug should I fiil a redmine? Thanks Stéphane

[gmx-users] Unable to generate .rtp file from gro and pdb file.

Dear Justin, I want to add the residue "hydroxyproline" or "HYP" in the OPLS AA in the aminoacids.rtp file . I have all the files of OPLS AA force field in my working directory. For that I tried to generate the initial rtp format file from the hydroxy proline's .pdb and .gro files using the

Re: [gmx-users] Periodic saving of checkpoint file

Hi, Since you are anyway intending to change the ensemble, you can just use nstxout, nstvout and nstenergy to write output every 10ps. That content is equivalent to that of the checkpoint. Use trjconv and eneconv afterwards to split those up, and use them as inputs to grompp -e -t along with the

[gmx-users] Periodic saving of checkpoint file

Dear all, I would like to run a long NVT simulation and save a checkpoint file every 10ps (in order to then run short NVE simulations from each checkpoint). Is there a way to save a .cpt file every 10ps in an automatic way? I can do it with other program, for example with Amber "ntwr=-5000" will

[gmx-users] Gromacs 2018.3 with CUDA - segmentation fault (core dumped)

Dear Gromacs Users, I have problem with my Gromacs 2018.3 that keeps crashing due to segmentation fault after quite long simulations time (more than 12 h wall clock). It is hard for me to tell why because there is no information why, except the segmentation fault message. Please find below

Re: [gmx-users] Correct use of gmx traj -mol ?

James, Have you tried the following? I interpret that to mean that the index fill will contain a group like this: [ Molecules ] i1 i2 i3 i4 i5 i6 ….. in Where each i term corresponds to a particular molecule within the system, and that number i will match up with the residue numbers. So can

[gmx-users] Correct use of gmx traj -mol ?

Hi, I am interested in obtaining temperature readings that are corrected for velocity (meaning, if a molecule has a net velocity, that kinetic energy should not be counted as part of temperature). I suspect this is what the traj -mol option would do, but I can't get it to run without error. I am