AMBER Archive (2005)

Subject: Re: AMBER: layer

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Fri Mar 18 2005 - 10:01:45 CST

you may still have problems with the approach- is there a reason you
are not doing a periodic simulation in a truncated octahedral box?
it will probably run much faster than something in a ball where you should
not use a cutoff, and you will not need any restraints. if you do use a
sphere of water, you probably want to include a reaction field treatment
of solvation beyond the sphere in order to have a good simulation.

===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

Gustavo Pierdominici Sottile wrote:

> Dear amber community,
> The system I study consists of a polipeptide chain solvated
> in a ball of water molecules. If I practice a dynamic without
> constraints in the solvent, water molecules go everywhere. If I do it
> with constraints, I see that bfactors are small as if the protein
> feels trapped in a cage. The solution would be to constrain only an
> outer layer of water molecules, can I do this? is there any keyword
> that allows me to contrain atoms from a certain distance of the center
> of the protein?
> Kind regards
> Gustavo

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