Re: Strange MD simulation results with GB solvation at high temp.

From: David A. Case <>
Date: Wed 11 Sep 2002 18:20:17 -0700

On Tue, Sep 10, 2002, Soonmin Jang wrote:
> Ans here is the run script I used
> &cntrl
> ntb=0, igb=1, ig=17436,
> imin=0, irest=0, ntx=1, tempi=300.0, ntt=1, temp0=604.0, tautp=0.5,
> nstlim=4000000, dt=0.001,
> ntwe=100, ntwx=500, ntpr=5000,
> &end
> Any comments will be appreciated.

I don't know if this is related to your problem, but using the default cutoff
(8 Ang.) is only recommended for PME calculations. Certainly a longer cutoff
would be needed for good simulations with gb. But it's not clear if or how
this is related to the temperature behavior you saw. It could be that you
have reached a situation where certain atom pairs are moving inside then
outside the cutoff repeatedly.

Note also that using a thermostat to control temperature for a very small
system (only five residues, no water) might lead to weird behavior.

..hope this helps...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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Received on Wed Sep 11 2002 - 18:20:17 PDT
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