[gmx-users] big protein dynamics

David van der Spoel spoel at xray.bmc.uu.se
Tue Dec 6 11:44:34 CET 2005

Adriana Pietropaolo wrote:

>thank you for your help, it's very kind from you help people who use 
>Now, I start the run, and I have a doubt.
>To rerun the simulation, I use the option rerun with the binary 
>Is it sufficient or it needs also a restart tpr file, for example if I 
>want to change the simulation time, I reprocessed the mdp file with 
>grompp, but the topology and the .gro file must be the last configuration 
>of my run, or I may use any .gro and .top configuration of my sample 
>because mdrun reads the .trr file?
mdrun does not read a trr file. You  probably want to do
tpbconv -e -s -f -o
grompp -t -e

>mdrun d

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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