[gmx-users] Simulated Annealing

Anton Feenstra feenstra at chem.vu.nl
Thu Jan 22 10:25:02 CET 2004

Martina Bertsch, PhD wrote:

> Sounds interesting. Would you, please, elaborate or perhaps send me the 
> part of the mdp file that programs the gradual release?

As with your annaeling scheme, this is not progammable in a single mdp file.
In stead, I use a shell script that runs grompp and mdrun repeatedly, in this
case with different posre*.itp files. For each group of atoms, starting with
the largest, I have a separate posre*.itp file that I use in the consecutive
grompp calls, and a corresponding series of #ifdef POSRE_* in the .top file.
It would look a little like this. There are a conf.gro, topol.top and grompp.mdp
file present, as well as several posre*.itp files (remember that conf.gro,
topol.top, grompp.mdp and topol.tpr are the default files names for grompp
and/or mdrun).

# step 1
grompp -f pr -D POSRE_ALL -o topol.tpr
mv conf.gro bf1.gro
mv confout.gro conf.gro

#step 2
grompp -f pr -D POSRE_ALL_BB -o topol.tpr
mv conf.gro bf2.gro
mv confout.gro conf.gro

#step 3
grompp -f pr -D POSRE_CORE -o topol.tpr
mv conf.gro bf3.gro
mv confout.gro conf.gro

#step 4
grompp -f pr -D POSRE_CORE_BB -o topol.tpr
mv conf.gro bf4.gro
mv confout.gro conf.gro

Note that in this case, only the initial .gro files (renamed to
'bf?.gro') of each step are kept, as well as the last confout.gro


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

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