[gmx-users] peptide out of box

[Rakesh Mishra]

hI

My -d parameter is 1.1 in editconf. Is that alright?

rakesh

On 3/13/07, Olivier Perin <operin at pasteur.fr> wrote:
>
> Hi,
>
> 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
>
> Olivier
>
> 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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