GROMACS version: Simulation: 2018.3, Analysis: 2022.5
GROMACS modification: No
Summary:
I have a weird .xtc file that causes trjconv -dt 100 to not write frames at the requested interval although the timestamps are in the ,xtc file. The timedeltas in the file are not consistent with alternating 8 ps and 12 ps timesteps between frames (despite having the nstxout-compressed in my .mpd file set to 10, but I think that error stems from filesystem issues on the HPC resource running the simulations).
Files:
traj_comp.xtc, topol.tpr
Step 1:
(prepare distance analysis by making an index of two atoms)
echo -e "a1 | a2\nq\n" | gmx make_ndx -s topol.tpr
Step 2:
(distance analysis)
gmx distance -f traj_comp.xtc -s topol.tpr -n index.ndx -oall dist.xvg
head -40 dist.xvg
# This file was created Thu Mar 2 17:23:19 2023
# Created by:
# :-) GROMACS - gmx distance, 2022.3 (-:
#
# Executable:
# Data prefix:
# Working dir:
#
# Command line:
# gmx distance -f traj_comp.xtc -n index.ndx -s topol.tpr -oall dists.xvg
# gmx distance is part of G R O M A C S:
#
# GRoups of Organic Molecules in ACtion for Science
#
@ title "Distance"
@ xaxis label "Time (ps)"
@ yaxis label "Distance (nm)"
@TYPE xy
38307920.000 0.293
38307928.000 0.244
38307940.000 0.298
38307952.000 0.272
38307960.000 0.302
38307968.000 0.291
38307980.000 0.254
38307992.000 0.309
38308000.000 0.324
38308008.000 0.288
38308020.000 0.346
38308032.000 0.298
38308040.000 0.234
38308048.000 0.292
38308060.000 0.255
38308072.000 0.279
38308080.000 0.259
38308088.000 0.249
38308100.000 0.277
38308112.000 0.326
38308120.000 0.315
38308128.000 0.290
38308140.000 0.275
38308152.000 0.274
38308160.000 0.262
38308168.000 0.255
38308180.000 0.262
38308192.000 0.251
38308200.000 0.288
38308208.000 0.276
38308220.000 0.234
38308232.000 0.269
38308240.000 0.244
Step 3:
(based on the timesteps in the file, I determine the start-time to be 38,308,000 ps and I execute):
echo -e "0\n0\n" | gmx trjconv -f traj_comp.xtc -s topol.tpr -b 38308000 -dt 100 -center -pbc nojump -o traj_comp_dt_100.xtc
Step 4:
(I then run the same gmx distance command on the traj_comp_dt_100.xtc file and expect all frames to be divisible by the requested -dt 100 ps)
head -40 dist_dt_100.xvg
# This file was created Thu Mar 2 17:45:25 2023
# Created by:
# :-) GROMACS - gmx distance, 2022.3 (-:
#
# Executable:
# Data prefix:
# Working dir:
# Command line:
# gmx distance -f traj_comp_dt_100.xtc -n index.ndx -s topol.tpr -oall dist_dt_100.xvg
# gmx distance is part of G R O M A C S:
#
# Getting the Right Output Means no Artefacts in Calculating Stuff
#
@ title "Distance"
@ xaxis label "Time (ps)"
@ yaxis label "Distance (nm)"
@TYPE xy
38308000.000 0.324
38308008.000 0.288
38308100.000 0.277
38308192.000 0.251
38308200.000 0.288
38308208.000 0.276
38308300.000 0.286
38308392.000 0.337
38308400.000 0.246
38308408.000 0.313
38308500.000 0.277
38308592.000 0.340
38308600.000 0.312
38308608.000 0.296
38308700.000 0.279
38308792.000 0.264
38308800.000 0.236
38308808.000 0.279
38308900.000 0.316
38308992.000 0.297
38309000.000 0.298
38309008.000 0.292
38309100.000 0.302
I can upload the files, if that would help in figuring out this error.
I am currently using MDAnalysis to create the dt 100 ps trajectory, but would like to do it with GROMACS.
Thank you in advance for your help