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/
> ==============================================
>
> _______________________________________________
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>
>
--
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
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Received on Wed Aug 08 2012 - 03:30:02 PDT
