AMBER Archive (2005)

Subject: AMBER: GB solvation and "boxed" environment simulation

From: Soo (protege_at_snu.ac.kr)
Date: Thu Feb 17 2005 - 23:32:38 CST

Hi All,

 

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

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

 

I know periodic boundary condition is not possible with GB (igb>0) but I
don't want periodic boundary condition. I just require some "confined" box
(could be cubic or sphere)  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.

 

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

 

Any suggestion is appreciated.

Thank you.

 

Soo

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