Re: AMBER: layer

From: Guanglei Cui <>
Date: Fri, 18 Mar 2005 10:13:32 -0500

Hi, Gustavo

How big is your force constant on the watercap? Generally, I found 0.5
kcal/mol is enough for most of the cases. The observed protein
fluctuation is roughly the same as in a periodic boundary calculation.


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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Received on Fri Mar 18 2005 - 15:53:01 PST
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