Re: [AMBER] restraints in igb simulation

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 17 Feb 2012 07:52:07 -0500

It completely depends on what you're trying to do.

Without that it's hard to give anything but the most generic (unhelpful) advice.

Think hard about the question you are trying to answer and what simulation details would be required to probe that.

HTH,
Jason

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Feb 17, 2012, at 1:21 AM, Danny Xu <quantum_mania.yahoo.com> wrote:
> Hello,
> 
> In an igb simulation, what would be a good approach to:
> 
> 1. restrain the protein to remove its rotation/translation, in another word, fix its center of mass
> 2. confine a ligand to move only inside a defined 3D box
> 
> Thanks very much in advance!
> 
> -DX
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Received on Fri Feb 17 2012 - 05:00:02 PST