[gmx-users] Re: Extending the simulation

bharat gupta bharat.85.monu at gmail.com
Fri Feb 11 13:55:44 CET 2011

Ya I found that the new trajectory is saved with name traj.trr and traj.xtc
... and I remember I saved the new tpr file as next.tpr..

Now I want to merge the two trajectories and the two .tpr files... I found
trjcat can be used ... I used the following command: -

trjcat -f1 md_0_1.xtc -f2 traj.xtc -o trjout.xtc

but its giving error ..

Can u tell me how to merge both the .tpr and .xtc files

On Fri, Feb 11, 2011 at 3:34 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 11/02/2011 8:10 PM, bharat gupta wrote:
> Hi,
>  I extended by 3ns simulation by 2 more ns ... i.e total 5 ns but the .xtc
> file shows only the 3ns trajectories and after checking the md.log file ,
> its showing that it completed those 2 ns steps also... then how can I get
> the trajectory for those 2ns ... I used the following commands for extending
> the simulation ...
>  tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
> mdrun -s next.tpr -cpi previous.cpt
> I do not understand how the next.log can show "that it completed those 2 ns
> steps also".
> The old .xtc files will probably have been renamed. Exactly what name
> varies with GROMACS version.
> Mark
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