AMBER: layer

From: Gustavo Pierdominici Sottile <gsottile.unq.edu.ar>
Date: Fri, 18 Mar 2005 11:42:53 -0300

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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