[gmx-users] extend MD runs

[Xavier Periole]

deepa rajamani wrote:

>Hi,
>
>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

-- 
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   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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