[gmx-users] Targeted Molecular dynamics

[Jay Mashl]

I have implemented one approach to targeted MD for version 3.2.1 that uses soft 
restraints to achieve the transformation.  We imagined we would make the code 
available (contribute it to Gromacs)  after we submit the manuscript.

Jay

-- 
R. Jay Mashl
University of Illinois
mashl at uiuc.edu
(Tel)217-244-5818


On Mon, 7 May 2007, Olivier Perin wrote:
> 
> Dear gmx users,
>
> OBJECT:
> 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.
>
> SITUATION:
> 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)?
>
> MY HYPOTHESIS:
> 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 
> struct2.pdb
>
> (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 
> struct1_DM1.pdb
>
> QUESTIONS:
> 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
> ------------------------------------