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
--
==================================================================
David A. Case | e-mail: case.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:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Tue Nov 11 2003 - 17:53:00 PST
