[gmx-users] how to make whole trajectory Pdb files

David van der Spoel spoel at xray.bmc.uu.se
Wed Mar 25 07:45:07 CET 2009

Bhawana Gupta wrote:
> Hello Everyone,
> Pls tell me after doing simulation, which command should i use ,so that 
> i can get all the pdb files of whole trajectory.
> I know the command where i can get one pdb file at a time,
> i.e.
> trjconv -f *_vac_md_1ns.xtc -s *_vac_md_1ns.tpr -dt 20 -b 0 -e 300 -o 
> _vac_md_1ns_300.pdb
> trjconv -f *_vac_md_1ns.xtc -s *_vac_md_1ns.tpr -o 
> *_vac_md_1ns_dump_300.pdb -dump 300
> This command will give me pdb file for 300ps file where my total 
> simulation is for 1 ns.
>  but how to get whole pdb files for the simulation of 1ns where my dt=0.2
> This is a very silly problem.
> But Please help me out.


> With Regards
> Bhawana
> ------------------------------------------------------------------------
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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