Re: RE: TAUP and density problem

From: David A. Case <>
Date: Mon 17 Feb 2003 10:06:03 -0800

On Mon, Feb 17, 2003, yuan bo wrote:
> The tempature vary very small in simulation and
> enery is not stable.

The fact tha the energy is not stable might be a clue, but is not very
specific. If you just run a short NVE simulation (say 10-20ps), is the total
energy conserved?

With the behavior you described, changing taup is not going to help much --
1.0 should be on OK value. I've never used organic solvents, maybe someone
else on the reflector has some useful experience. Note that it may be
that the "correct" density for your solvent with all bonds shaken differs
from that for a "floppy" solvent where not all bonds are shaken.

..good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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Received on Mon Feb 17 2003 - 10:06:03 PST
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