[gmx-users] Extent and append the out put with out presence of .trr file

Mark Abraham mark.j.abraham at gmail.com
Tue Jan 24 11:44:32 CET 2017


You don't have to append via the automated mechanism :-) mdrun refuses to
do so, in order that you can't accidentally do something you didn't intend.
But mdrun -noappend will extend the simulation in exactly the same way,
while writing files that include the part number. You'll then have to
handle any concatenation yourself, but that's the price of having software
that makes it hard to do things that you might regret.


On Tue, Jan 24, 2017 at 8:40 AM Alex <alexanderwien2k at gmail.com> wrote:

> Hello gromacs user,
> I would like to extent a simulation by increasing the number of steps and
> appending the results, unfortunately, I have already delete the .trr file
> but *.xtc file and the rest are present.
> So, I am invoking below commands first to extent the number of step and
> then to run and append the simulation:
> mpirun -x PATH -np 1 gmx_mpi convert-tpr -s prd.tpr -e prd.edr -nsteps
> 26000000 -o prdNW.tpr
> mpirun -x PATH gmx_mpi mdrun -ntomp 1 -s prdNW.tpr -deffnm prd. -pf
> pullf-prd. -px pullx-prd. -cpi prd.cpt -append
> It complain about missing *.trr file while appending.
> The simulation is a one windows of PMF simulation and I want to append the
> outputs?
> I was wondering how I can extent the simulation and append the outputs with
> missing the *.trr file without loosing the accuracy?
> Regards,
> Alex
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