[gmx-users] Re: Extending the simulation
Justin A. Lemkul
jalemkul at vt.edu
Fri Feb 11 13:58:40 CET 2011
bharat gupta wrote:
> 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 ..
You're not supplying valid command line flags; -f1 and -f2 don't exist. See
> Can u tell me how to merge both the .tpr and .xtc files
There is no need to merge .tpr files, nor can they be.
> On Fri, Feb 11, 2011 at 3:34 AM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
> On 11/02/2011 8:10 PM, bharat gupta wrote:
>> 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.
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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