[gmx-users] Defining protonation in pdb2gmx input

This is continuing a thread from a month ago. Quoting Justin Lemkul : Now I did a bit more testing, and at least renaming ASP to ASPH in the input will get me an ASPH in the output, but only the residue name, not the hydrogen. So I get a residue named ASPH, but the structure is an

[gmx-users] gmx rms vs. trjconv

I ran into what seems to be a bug, namely that the -skip option in gmx rms doesn't seem to do anything. The output always has the RMSD values for all frames, even if -skip is specified. I filed a bug (https://redmine.gromacs.org/issues/2565). Then I resorted to trjconv to do the skipping

[gmx-users] gmx rms vs. trjconv

Never mind my previous question about using trjconv for fitting in RMSD calculations. It does produce identical results compared to using gmx rms alone. I just had a subtle error in atom numbering, which resulted in bogus RMSD values. -- Gromacs Users mailing list * Please search the

Re: [gmx-users] how to reassign velocities in the .mdp file effectively?

I am trying to test the reproducibility of the md production run. You can use the options gen-vel = yes gen-temp = 300 gen-seed = -1 in your .mdp file and run again. That example will generate new random velocities corresponding to 300 K and

Re: [gmx-users] Definiting protonation in pdb2gmx input

Quoting Justin Lemkul : problem. Please file a bug report on Redmine and include example input files and pdb2gmx syntax you're using. Ok, thanks. Bug posted at https://redmine.gromacs.org/issues/2480 -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Definiting protonation in pdb2gmx input

One of the recurring questions on the list seems to be how to define residue protonation states non-interactively in pdb2gmx input. The interactive options are a bit of a nightmare to use. Could pdb2gmx be modified to optionally read the residue types from the PDB file itself? The user

Re: [gmx-users] Definiting protonation in pdb2gmx input

Quoting Justin Lemkul : I just tested this in GROMACS 2018 and it works fine - if you provide the protonated residue name, pdb2gmx correctly interprets the protonation state. Do you have a use case that fails? Is this behavior documented somewhere? I don't seem to find any