AMBER: GB solvation and "boxed" environment simulation

From: Soo <protege.snu.ac.kr>
Date: Fri, 18 Feb 2005 14:32:38 +0900 (KST)

Hi All,


&nbsp;


I am using Amber8. I think I asked similar question before.


Is it possible to do simulation with the GB( Generalized Born, igb&gt;0
)&nbsp;solvation model under the "boxed" environment ?


&nbsp;


I know periodic boundary condition is not possible with GB (igb&gt;0) but I
don't want periodic boundary condition. I just require some "confined" box
(could be&nbsp;cubic&nbsp;or&nbsp;sphere) &nbsp;just like reflecting boundary
condition implimented in TINKER Package (option name "wall") so that the
molecules can not escape within given distance. Maybe harmonic restraint from
the center of mass is OK.


&nbsp;


"Watercap" is not an option since it seems to me this option works only with
explict solvent (water).


&nbsp;


Any suggestion is appreciated.


Thank you.


&nbsp;


Soo










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Received on Fri Feb 18 2005 - 05:53:00 PST
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