AMBER Archive (2005)

Subject: Re: AMBER: using position restraints in target MD?

From: Viktor Hornak (hornak_at_csb.sunysb.edu)
Date: Fri Oct 21 2005 - 15:14:42 CDT


Dear Ben,

As you're obviously using Amber8, you can use positional restraints as
usually, with ntr=1 and restraint mask and weight set...

Cheers,
-Viktor

Ben-Zhuo Lu wrote:

> Dear Amber users,
> I'm wondering if we can use position restrains in the
> the target MD simulation. In TMD, both the parts defined by tgtfitmask
> and tgtrmsmask will be affected, but sometimes, we want to keep
> most part (not the masked part by tgtrmsmask) of the simulated system
> stable.
> Then, how to do it?
>
> Thanks,
>
> Ben.
>
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-- 
===================================================================
Viktor Hornak
Center for Structural Biology   Phone: (631)632-1439
SUNY at Stony Brook             Fax:   (631)632-1555
Stony Brook, NY 11794-5115      E-mail: viktor.hornak_at_sunysb.edu
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