RE: AMBER: MD run: frozen

From: Ross Walker <>
Date: Sat, 27 Nov 2004 23:00:37 -0800

Hi Bo,

> I am running MD simulation on my protein model with implicit
> solvent. The protein was solvated with WATBOX 216.

Please re-read this sentence and the problem should become obvious to you.

> ntt=1, tempi=0.0, temp0=310,o, tautp=2, ig=209858,

What is the ,o, here???

> ntp=0, igb=1,
> ntb=0, ntc=2, ntf=2,

You use a water box but have ntb=0 and igb=1 (think about this).

> nstlim=5000, ntwx=5000, ntpr=500,

Try setting ntpr=1 and you will see that your calculation is not frozen, it
is just running very slowly. The reason it is running so slowly is that the
EGB routine is not very efficient with >1000 atoms or so. And you have given
it a protein in a "BOX" of water...

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Sun Nov 28 2004 - 07:53:00 PST
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