On Mon, Dec 22, 2003, Wayne Dawson wrote:
>
> I am trying to study solvent effects on an electrostatic protein.
> I have a structure I obtained, and I have done simulations on
> this thing out to ns using SHAKE. But I want to look at some
> simulations without SHAKE (i.e., setting ntc=1).
>
> I simply cannot seem to run sander successfully with ntc=1. I've
> already equilibrated this protein under NPT conditions out to 0.250 ns
> using SHAKE, yet I still keep failing because of problems with
> exceeding the vlimit. I've tried time-steps as short as 0.1
> fs. Nothing seems to stabilize the calculation.
>
> I can definitely calculate this same kind of simulation on Discover
> (Amber 6) with comparable conditions (below). I want to check these
> Discover results using TIP3P water and amber7. What am I doing wrong?
The TIP3 water model was defined to be a rigid model. If you allow the bond
lengths to change it can find regions of conformational space where a hydrogen
on one water molecule gets arbitrarily close to an oxygen on another, leading
to negative inifinities in energies. Even if this doesn't happen, the
properties of such a "non-rigid TIP3" will not be the same as "real" TIPE. So
it is neither correct nor necessarily practical to run TIP3 simulations in
Amber without using SHAKE.
(Generally, however, short simulations do not blow up the way yours did. I
am concerned that your initial pressures are so different from unity. You
could try a much longer taup value, at least an order of magntiude larger,
and see if this helps.
...good luck...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 Wed Jan 14 2004 - 15:53:11 PST
