Re: [gmx-users] restarting the crashed run

[Mark Abraham]

Hi,

The default name for that file is confout.gro, which it will be unless you
chose a different name with

gmx mdrun -c nvt.gro

or

gmx mdrun -deffnm nvt

However, you can sometimes
get slightly better results by using

gmx grompp -c whatever -p topol -t nvt.cpt -f npt -o npt

because now the box, coordinates and velocities are read at full precision
from the nvt checkpoint, unlike when you read the npt gro file.

Mark

On Mon, Oct 3, 2016 at 5:39 AM Roshan Shrestha  wrote:

> I had restarted my crash run for NVT equilibration using* gmx mdrun -s
> nvt.tpr -cpi nvt.cpt -v *, the simulation restarted and finished fine, but
> at the end of the simulation I did not get my nvt.gro, which I needed to do
> further NPT equilibration. Where is nvt.gro ? Did I do something wrong, or
> the file has been renamed to something ? Please suggest me. Thanks
>
>
> --
> Roshan Shrestha
> Graduate Student
> Central Department of Physics,Tribhuvan University
> Kathmandu,Nepal
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> Gromacs Users mailing list
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[gmx-users] restarting the crashed run

[Roshan Shrestha]

I had restarted my crash run for NVT equilibration using* gmx mdrun -s
nvt.tpr -cpi nvt.cpt -v *, the simulation restarted and finished fine, but
at the end of the simulation I did not get my nvt.gro, which I needed to do
further NPT equilibration. Where is nvt.gro ? Did I do something wrong, or
the file has been renamed to something ? Please suggest me. Thanks


-- 
Roshan Shrestha
Graduate Student
Central Department of Physics,Tribhuvan University
Kathmandu,Nepal
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Re: [gmx-users] Restarting a crashed run

[vaani]

hi ..i am having same problem as you did..can you please suggest how you
solved it ???


-
thanks in advance :)
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Re: [gmx-users] Restarting a crashed run

[bharat gupta]

If you have done the same mistake what I did, then you should get two files
with names traj.xtc and traj.trr. These files contains the results for the
restarted simulation. You can use trjconv to concatenate the new
(traj.xtc)+ previous(old.xtc) files. I hope this should work for you...


On Mon, Dec 30, 2013 at 3:35 PM, vaani vsha...@imtech.res.in wrote:

 hi ..i am having same problem as you did..can you please suggest how you
 solved it ???


 -
 thanks in advance :)
 --
 View this message in context:
 http://gromacs.5086.x6.nabble.com/Re-Restarting-a-crashed-run-tp4456957p5013569.html
 Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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