[gmx-users] peptide out of box

Olivier Perin operin at pasteur.fr
Tue Mar 13 08:34:26 CET 2007


4ns becomes a long dynamic simulation. Sometimes during such a 
simulation, the system moves such a way that it "seems" to get out of 
the water box.

In order to prevent this phenomen, you can use one parameter normally 
used during a simulation in vaccum:

nstcomm             = 500         ;

You can add this line to your mdp file before the grompp step. This is 
the frequency for center of mass motion removal.

About the 2.2nm: if it is the real size of your box, I agree with the 
answer of Mark, the box is probably to short. But if it's your "-d" 
parameter for editconf, it is largely sufficient.

Good Luck


Mark Abraham a écrit :
> Rakesh Mishra wrote:
>> When I run simulations on a 42 residue peptide with a box size of 2.2 
>> nm , I find that after 4 ns , the peptide comes out of the box . Is 
>> this a problem as far as the accuracy of the simulation results are 
>> concerned. Do the periodic conditions account for such cases? If not 
>> , is there any suggestion as to how I may salvage my data without 
>> having to start all  over again .
> The peptide can't "come out of the box" - the system is periodic. The 
> numbers in the trajectory file can be such that your visualization 
> software will render an image that looks like the peptide comes out of 
> the box, however. Look at the man page for trjconv and choose an 
> option appropriate for your situation and use that on the trajectory 
> before visualizing.
> By the way, a 42 residue peptide is almost certainly too large for 
> such a box, even if it is a compact peptide. There are guaranteed to 
> be many water molecules (or even all of them) that are having 
> non-bonded interactions with two images, which is unphysical.
> Mark
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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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