AMBER Archive (2003)

Subject: Re: AMBER: restraints and reordering water

From: David A. Case (case_at_scripps.edu)
Date: Tue Nov 11 2003 - 11:21:10 CST

On Tue, Nov 11, 2003, Vlad Cojocaru wrote:

> I have a simulation which ran for 7ns (explicit solvent, PME,
> Periodic). The structure pretty stable. Now I want to introduce a
> restraint over the next 2-3 nanoseconds. I have several questions:
> 1. Can I do that straight away by just restarting the simulation
> starting from the last rst file but using as sander input the file
> containing the restraint? Or do I have to consider some other steps
> before that?

Nothing else is needed.

> 2. If I have a DISANG file with the restraint it seems that I need a &wt
> list. I took a look at the manual and the only thing that I found was
> the&wt type='REST' option that is applicable in my case. Could somebody
> shortly explain me how this works with "Ramping up the restraints", is
> that necessary or can I go with a constant manner of applying the restraint?

This depends on the physics and chemistry of your problem.

> 3. I got a mssage that "Reordering water will NOT be done" if nmropt>0,
> is that ok and what actually does it mean?

Just an informational message; don't worry about it.

..dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
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