IMO, a better solution would be to use cpptraj and the "autoimage" function
(make sure you have up to AmberTools bugfix.19 applied -- you can check
this via $AMBERHOME/patch_amber.py --patch-level) on the troublesome
restart file. This will move your protein back to the center of the box
and re-image your solvent and other small molecules around it.
It should also keep velocities intact, so you should be able to continue MD
from there without any issues.
HTH,
Jason
On Wed, Aug 8, 2012 at 7:27 AM, Anselm Horn <
Anselm.Horn.biochem.uni-erlangen.de> wrote:
> Hi Fernando,
>
> maybe fixing one of the respective atoms to its position with harmonical
> restraints would be an option. With this you'd prevent your molecule, or
> at least the interesting part, from leaving your box.
>
> However, I've never done this and am not sure whether this introduces
> too much perturbation on your system.
>
> Regards,
>
> Anselm
>
> Bioinformatik
> Institut für Biochemie
> Friedrich-Alexander-Universität Erlangen-Nürnberg
> Germany
>
> Am 08.08.2012 12:35, schrieb Fernando Martín García:
> > But, if I understood well, iwrap doesn't resolve the high diffusion of
> > the protein in the box (and I proved with iwrap=1 too). So, the only
> > solution is to enlarge the box size? Is there any other possibility?
> >
> > Thanks,
> >
> > Fernando
> >
> > On Wed, 8 Aug 2012 12:13:51 +0200, Jérôme Golebiowski wrote:
> >> If you are performing an umbrella sampling and this extends your
> >> molecule to
> >> larger value than your box size, you should enlarge your box.
> >> Otherwise, maybe just setting iwrap to 1 will help keeping the
> >> protein close to
> >> the box center.
> >> HTH.
> >> Best,
> >> Jerome
> >>
> >>
> >>
> >> Selon Fernando MartÃn GarcÃa <fmgarcia.cbm.uam.es>:
> >>
> >>> Dear Amber users,
> >>>
> >>> I have a "technical" problem with a distance restraint. I'm working
> >>> with a protein with a 12 angs. TIP3 box. The simulation time is 30
> >>> ns.
> >>> After 20 ns, a small part of the protein is out of the box. The
> >>> problem
> >>> is that one of the residues out of the box has a restrain with one
> >>> residue in the part of the protein inside the water box, so the
> >>> value
> >>> changes, what it causes a high restraint value. Is there any
> >>> solution
> >>> for this?
> >>>
> >>> Thanks
> >>> --
> >>> ==============================================
> >>> Fernando MartÃn GarcÃa
> >>> Molecular Modelling Group - Lab 312.1
> >>> Molecular Biology Center "Severo Ochoa"
> >>> C/ NICOLáS CABRERA, 5.
> >>> UAM University. Cantoblanco, 28049 Madrid. Spain.
> >>> TEL: (+34) 91-196-4662 FAX: (+34) 91-196-4420
> >>> Web: http://fertoledo.wordpress.com/
> >>> ==============================================
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>>
> >>
> >>
> >> --
> >> Jérôme Golebiowski
> >> Institute of Chemistry - Nice
> >> Molecular Modeling Team
> >> UMR 7272 CNRS, University of Nice Sophia Antipolis
> >> 06108 Nice cedex 2, France
> >>
> >> tel: +33 (0)4 92 07 61 03
> >> http://www.unice.fr/icn
> >> http://www.unice.fr/icn/golebiowski
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> _______________________________________________
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Aug 08 2012 - 05:30:03 PDT
