[gmx-users] Re: Extending the simulation

[Justin A. Lemkul]

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 
trjcat -h.

> 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.

-Justin

> 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:
>>     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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> 
> 
> -- 
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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