[gmx-users] continual running

[chiloo Laohpongspaisan]

David,
 
Are there any options for continual run which supports in gromacs 3.1.1? or I need to change into 3.2.1 version only

Best regards,
Chiloo

David <spoel at xray.bmc.uu.se> wrote:
On Sun, 2005-08-07 at 23:20 -0700, chiloo Laohpongspaisan wrote:
> Dear All,
> 
> How can i countinue the running of next MD with the last configuration
> of previous MD (i use the Gromacs version 3.1.1). if I ran MD 1000 ps
> already, and i'd like to run more 1000 ps with the last configuration
> of the previous MD (so, the last configuration (.gro file )at 1000ps
> of the previous MD is the same as the 1st configuration at 0 ps of the
> next MD, that's right?)
tpbconv -f -s -o -until 2000
maybe you should add -e as well if that's supported in 3.2.1

> 
> I tried to use normal step to run the next MD, but the velocity seems
> not to be the same.
> this is my brief procedure:
> -extract the configuration at 1000 ps of previous MD: trjconv -f
> traj.trr -s md.tpr -o md-1000.gro -b 1000
> -use grompp to prepare the new file.tpr: grompp -f md.mdp -c
> md-1000.gro -p top.top -o md2.tpr
> -run MD: mdrun -s md2.tpr -o traj.trr -c pmd2.gro -g md2.log -e
> md2.edr &
> Please check it for me, what's wrong ?
> 
> Best regards,
> Chiloo
> 
> 
> 
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-- 
David.
________________________________________________________________________
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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