Re: AMBER: problem of the REMD with nmr constraints

From: wenfei Li <wfli.biophy.nju.edu.cn>
Date: Fri, 8 Dec 2006 08:55:04 +0800

Dear Prof. Simmerling,

The amber9 works well with this option.

Thank you very much!

Wenfei Li

NJU PRC

----- Original Message -----
From: "Carlos Simmerling" <carlos.csb.sunysb.edu>
To: <amber.scripps.edu>
Sent: Friday, November 24, 2006 10:35 PM
Subject: Re: AMBER: problem of the REMD with nmr constraints


> can you try amber9 to see if this problem still happens?
>



> wenfei Li wrote:
> >Dear AMBER users,
> >
> > I'm performing a replica-exchange MD simulation for a zinc ion containing protein system using AMBER8. The zinc ion is not bonded to any residue.
> >
> > When I add the nmr constraint (distance constraint) between the zinc ion and the protein atoms by setting nmropt=1, the exchange behavior is abnormal: the temperatures of each replicas can only be switched to their very near neighbors and then come back to their original values quickly. But, when without the nmr constraint, the exchange behavior is normal: the temperatures of each replicas can variate within a wide temperature range randomly.
> >
> >Is this a bug or something wrong with my input parameters?

> >NJU, PRC
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Received on Fri Dec 08 2006 - 16:23:22 PST
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