Restarting simulation without the checkpoint file ( *.trr doesn't contain coordinates)

User discussions
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1

GROMACS version: 2019.6
GROMACS modification: No

Hi everyone!

I have a 200ns simulation and I want to continue a simulation from 160ns. I don’t have the checkpoint file because 160ns is not the last frame of the simulation. Since I need at least coordinates and velocities to continue the simulation, one way is to dump 160ns as a .gro file from the .trr file. Another way is to use grompp with .trr for -t. However, in my mdp file, coordinates are set to be written in xtc file and .trr file doesn’t contain coordinates. In this situation, none of the ways I said works! In the following lines, I shared my command lines and outputs.

When I use -dump :

gmx_mpi trjconv -f traj_160ns.trr -s tpr.tpr -dump 160000 -o 160ns.gro

( I extracted .trr of 160ns, named traj_160ns.trr which contains velocities of 160ns, not coordinates)

I get this output:

Select group for output
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.
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Select a group: 0
Selected 0: ‘System’
trr version: GMX_trn_file (single precision)
*Last frame -1 time 0.000 *

WARNING no output, last frame read at t=160000

So there is no output!

Or when I use grompp:

gmx_mpi grompp -f prod.mdp -c conf_160ns.gro -r conf_160ns.gro -t traj_160ns.trr -p topol.top -o test.tpr

I get this output:

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Note that mdrun will redetermine rlist based on the actual pair-list setup
Reading Coordinates, Velocities and Box size from old trajectory
Will read whole trajectory
trr version: GMX_trn_file (single precision)
*Last frame -1 time 0.000 *

WARNING: Did not find a frame with velocities in file traj_160ns.trr,

  •     all velocities will be set to zero!*

*Last frame -1 time 0.000 *

-------------------------------------------------------
Program: gmx grompp, version 2019.6
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 709)

Fatal error:
Did not find a frame with coordinates in file traj_160ns.trr

It doesn’t find velocities and also needs coordinates which are not provided in the .trr file.

Here is the check output of traj_160ns.trr:

Command line:

  • gmx_mpi check -f traj_160ns.trr*

Checking file traj_160ns.trr
trr version: GMX_trn_file (single precision)
*Reading frame 0 time 160000.000 *
# Atoms 720084
*Last frame 0 time 160000.000 *

Item #frames Timestep (ps)
Step 1
Time 1
Lambda 1
Coords 0
Velocities 1
Forces 1
Box 1

These commands work perfectly if .trr file contains coordinates as well. But now my .trr doesn’t have coordinates and I haven’t found any solution to continue my simulation from an arbitrary frame. Is there anything that I can do? Or am I using something wrong here?

Many thanks,
Hoda

2

Hi,
to extract velocities from trr file you can try
https://manual.gromacs.org/current/onlinehelp/gmx-traj.html
or
https://manual.gromacs.org/current/onlinehelp/gmx-trajectory.html
\Alessandra