[gmx-users] extend MD runs

Xavier Periole x.periole at chem.rug.nl
Mon Jul 19 11:01:53 CEST 2004

deepa rajamani wrote:

>What would be the best way to extend MD runs. I have the following issues
>1. I would like to break up long MD runs into shorter runs.
trjconv -f traj.xtc -b "start" -e "end", start and end are in ps.

>2. I want to minimize the slow backbone shift that occurs when I restart
>the simulations from the last saved frame of the previous run
Use the tpbconv -f traj.trr -s topol.tpr -extend or -until to extend the 
length of your
simulation. The same reference configuration shoul be used.

>3. I place hormonic constraints on the backbone atoms to avoid large
>movements of backbone, but there obviously, is a slow shift when I do MD
>in short runs instead of one long MD.
Same as before.



   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   Nijenborgh 4
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: http://md.chem.rug.nl/~periole

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