[gmx-users] extended calculation pdb extracttion query

[Justin Lemkul]

On 9/20/17 8:39 AM, Deep kumar wrote:
> Hi All,
> 
> I have run an extended simulation for 90ns like this: (my previous run was
> for 10ns)
> 
> grompp -f new.mdp -c old.tpr -o new.tpr
> mdrun -s new.tpr -cpi old.cpt
> 
> 
> because, I had to make changes in the .mdp file. I have got new files
> from the new extended run;
> 
> 
> new.tpr, new.xtc  ....etc
> 
> 
> My 10ns mdrun results are like old.tpr, old.xtc   ...etc
> 
> Now, I want to get the pdb files from the runs (10ns + 90ns). Can you
> please let me know how can I do it? I know to get the pdb files from mdrun
> I should do this:
> 
> gmx trjconv -s new.tpr -f new.xtc -dt 100 -o trj.pdb
> 
> but I want to combine both 10ns and 90ns and get the pdb files.
> 

This is what trjcat does.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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