[gmx-users] Targeted Molecular dynamics

Olivier Perin operin at pasteur.fr
Mon May 7 12:33:01 CEST 2007

Dear gmx users,

I just contact you to confirm one thing about the ability to run a 
targeted molecular dynamic simulation with gromacs with the help of 
positional restraints.

If struct1 and struct2 are two near conformations of one same protein 
could I use these two gromacs commands in order to force the first 
system (struct1) to direct to the second system (struct2)?

pdb2gmx -f struct1.pdb -i posre.itp -posrefc 1000 -p struct1.top

grompp -f MD_050K.mdp -c struct1.pdb -p struct1.top -o struct1_MD.tpr -r 

(for me, the option -r of grompp allowed to define with which 
coordinates the positional restraints must be set)

mdrun -s struct1_MD.tpr  -o struct1_MD.trr   -x struct1_MD.xtc  -c 

Do these commands seems to be correct?
What do you think about 1000 for positional restraints? Is it to high?

Thank you all for your answers!

Olivier PERIN - Institut Pasteur
Unite de Bioinformatique Structurale
25-28, rue du Dr Roux 75724 Paris Cedex 15
Tel: +331 40 61 38 84
Fax: +331 45 68 87 19
mail: operin at pasteur.fr

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