[gmx-users] rerun of trajectory!

Paul Barrett barrett at biop.ox.ac.uk
Wed May 14 12:50:01 CEST 2003

It looks right...

I use 

  tpbconv -s post_pr.tpr -f main.trr -o main_restart

  nohup mdrun -v  -s main_restart -o main_restart -x main_restart -c
main_restart -g main_restartlog >& main_restart.job

which works fine

Im sure you have already checked the following:
1) are you executing the command from the same working directory as
2) you did call the previous run traj.trr and not traj.xtc or traj.trj
or somethingelse.trr?
3) if traj.trr is in the directory where you are running it try

 ls -l traj.trr 

and see if it has a non-zero file size.

If all those are fine I cant think what the problem is.


Paul Barrett

>dear gromacs users,
>i'm trying to simulate a protein solvated in water.I ran the simulation
>for 1ns.This was successfully done.Now i want to continue the MD for
>another 9ns with the trr file of the 1ns simulation.
>So i tried making a continuation input file using tpbconv.i.e
>>tpbconv -s b4md_emsd_saksol.tpr -f traj.trr -n md_emsd_saksol.ndx -o
>But the command does not seem to work. My .trr file does not seem to be
>getting recognized. i'm getting the following error after running the tpbconv
>Reading toplogy and shit from b4md_emsd_saksol.tpr
>Reading file b4md_emsd_saksol.tpr, VERSION 3.1.4 (single precision)
>Reading file b4md_emsd_saksol.tpr, VERSION 3.1.4 (single precision)
>Modifying ir->bUncStart to TRUE
>Fatal error: File traj.trr not found
>Do i have to give any other option in the tpbconv command.
>Can anyone please tell me how i can make a continutaion input file for
>further rerun of the MD.
>Or if i take the output gro file created from the previous 1ns simulation
>and use it as input for the grompp command for the 9ns simulation, will it be
>equivalent to rerunning from where i left off. Or will the velocities and
>energies calculated in the trr file of the 1ns simulation change now as
>fresh initail velocities will be assigned for the new run.
>will really appreciate if someone can tell me how to go about it and what
>exactly can be done to solve the problem.
>Thanks & Regards ,
>Swetha Vijayakrishnan
>Swetha Vijayakrishnan
>Project Assistant
>C/O Dr.Shekhar.C.Mande
>Centre for DNA Fingerprinting and Diagnostics(CDFD),
>ECIL Road,Nacharam,
>Hyderabad - 500076
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