[gmx-users] extended calculation pdb extracttion query
jalemkul at vt.edu
Thu Sep 21 15:45:02 CEST 2017
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 A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
More information about the gromacs.org_gmx-users