[gmx-users] dynamic search and simulated annealing

David van der Spoel spoel at xray.bmc.uu.se
Thu May 26 08:52:56 CEST 2005

On Thu, 2005-05-26 at 08:36 +0200, UCT Staff Member - Jackson wrote:
> Dear Users
> I want to use high temperature molecular dynamics to search
> conformational space.  The protcol is to do a long run and collect 100
> structures on the way.  I then need to do simulated annealing on each of
> those 100 structures.  Simulated annealing on one structure is easy but
> how do I get mdrun to repeat the process on each of the structures in
> the trajectory?  

You will have to write a script that does hundred mdruns. 
trjconv -f traj -s topol -o conf.gro -sep -dt XXX
will give you N conformations (traj length/XXX) named conf_N.gro

set i = 0
while ( $i < N )
grompp -c conf_$i 
mdrun -o traj$i etc.
@ i ++

> Thanks
> Graham
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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