[gmx-users] peptide out of box

[Tsjerk Wassenaar]

Hi Rakesh,

That means that your box dimensions are 2*1.1 + dimensions of peptide.
This is bound to be more than 2.2 nm. 1.1 should be good enough
usually.

Tsjerk

On 3/13/07, Rakesh Mishra <rakesh1986 at gmail.com> wrote:
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623