Re: Problem in run

From: David Case <>
Date: Fri 8 Nov 2002 23:33:27 -0800

On Sat, Nov 09, 2002, Monica wrote:

> I am running DRUG-DNA complex using NMR distances in explicit water.
> Minimization was done successfullt but when I am running initial
> equilibration it gave following error
> Rescaling velocities by 35.16041

This is pretty scary! My best guess is that you are using amber6 (?)
and that you set ntt=4 (?) That will only work for an equilibrated
system...I recommend ntt=1 for intial equilibration.

(Actually, I don't know of any situation where ntt=4 is a desirable option;
that's why it has been removed from current versions of sander.)

Of course, my guesses could be way wrong (basically, I searched the code
for your error message....). If you have problems in the future, please
give more information about what you did.


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Fri Nov 08 2002 - 23:33:27 PST
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