GROMACS modification: No
Here post your question I have performed a short simulation of a peptide in a 50 by 50 by 100 Angstrom box.
It has completed and the automatically generated xtc file was written throughout. I am trying t omake a new xtc from the trr with the solvent removed, ie the protein only (Although I get the same lack of output when I try to write the whole system). I called trjconv as below
gmx_2019 trjconv -s unf_sub_0_eq.tpr -f unf_sub_0_eq.trr -o unf_sub_0_eq.xtc -center -pbc nojump
and selected the protein from the index list when prompted for centering and for output. The peptide was correctly read from the tpr file as the number of atoms in the group was correct.
it came back as below
trr version: GMX_trn_file (single precision)
Last frame -1 time 0.000
Setting output precision to 0.001 (nm)
WARNING no output, last frame read at t=100000
what is wrong please? I usually have no such issue with this approach
gmx check instead of
gmx dump, but likely no coordinates were saved in the
.trr file (i.e.
nstxout = 0, the default), so there’s nothing to write.
I used charm GUI to generate the input for the MD, usually I have only done so for membrane proteins and the trr file has been a suitable input for trjconv. Is the default option you speak of only default in soluble proteins? Is it a setting I can change in the MDP file? For my purposes in this case the automatically generated xtc was sufficient as input for trjconv, but it was bewildering why the things I am accustomed to doing suddenly didn’t work.
Look at the
.mdp options in the input files provided by CHARMM-GUI. That will tell you what you should expect in the output. Different modules sometimes have different output settings for no real obvious reason, but no, settings are not at all tied to membrane vs. soluble proteins. You can choose to print whatever output you want. The
.trr format is not generally all that useful unless you need velocities and forces and will eventually be removed from GROMACS, so this is likely why it is not being produced by CHARMM-GUI.
Thanks for your responses, the issue didn’t prevent me getting what I needed in the end this time. Hmm, the .trr file is being produced and is large - just the trjconv using the trr file as input delivers no output. Oh right, in the future how will one be able to access velocities and forces? will they be included in the xtc instead or something?