AMBER Archive (2003)

Subject: Re: AMBER: ndfmin in belly runs

From: David A. Case (case_at_scripps.edu)
Date: Thu Nov 13 2003 - 10:07:14 CST

On Thu, Nov 13, 2003, John wrote:
>
> Following on from Rhonda's e-mail I would appreciate it if you could provide
> me with some more information on the ndfmin when undertaking belly runs. I
> have not encounter this in any belly run so I assume that sander set this to
> 0. Do we have to subtract the degrees of freedom lost due to belly from the
> whole system? How does this change the ndfmin?

In sander 7, the ndfmin variable is not needed because it is set automatically
by the program. You can look at the code in mdread.f and runmd.f to see
what choices it is making, but they should be the correct ones.

This is a change from earlier versions, where the user was required to figure
out and set the correct value. However, the error caused by choosing an
incorrect value (say 0 rather than 6 or vice-versa) would be negligible for
biomolecular simulations with thousands of atoms.

> ndfmin =0 (default) is recommended, unless you are performing a
> belly run, etc. See p.167 in Amber 7 manual.

Note that the above comment refers to gibbs, not to sander.

..hope this helps...dac 

-- 

==================================================================
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:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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