[gmx-users] Targeted Molecular dynamics

Berk Hess gmx3 at hotmail.com
Mon May 7 13:41:35 CEST 2007

>From: Mark Abraham <Mark.Abraham at anu.edu.au>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] Targeted Molecular dynamics
>Date: Mon, 07 May 2007 21:20:23 +1000
>Olivier Perin wrote:
>>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)?
>It will take a finite number of MD steps to get arbitrarily close to 
>struct2, but yes this should work.
>>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?
>I suspect so, but if they are too high, then something in the structure 
>will break fairly quickly. If it's a complex structural change, then 1000 
>is almost certainly too high. Try it and see :-)

They might be correct, but this is an extremely rough way to do
targeted MD.
The manual decribes how to do it more properly.


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