On Thu, Aug 09, 2007, Nikola Trbovic wrote:
>
> I have run a couple of 20 ns NVE simulations of a protein in tip3p water
> with a parallel installation of the amber9 pmemd. I first equilibrated
> the system in an NPT simulation (ntt=1) and then started the NVE
> production runs from different starting structures extracted from the
> equilibrated part of the simulation with
>
> ntt=ntp=0, ntc=ntf=2, ntb=1 and cut=10.
>
> Over 20 ns Etot rose absolutely linearly and with barely any random
> fluctuations from ~-76660 to ~-75880. Over the same period the
> temperature rose from an average value of ~300 K to an average value of
> ~305 K.
Sorry to be late in chiming in here. As others have said, to get good energy
conservation, you almost certainly need to use dt=0.001 and SHAKE with a tight
tolerance. Reducing the dsum tolerance (as Tom Cheatham) suggested, also
helps.
As a data point, I have run 100 ns NVE simulations of small proteins, and
we do see a very progressive energy drift, but with a change of about 0.5 K
over 100 ns. I haven't tried long simulations myself with dt=0.002, but my
guess is that is the principal "culprit" for you.
...regards...dac
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Received on Sun Aug 12 2007 - 06:08:10 PDT
