Thank you for chiming in at all! I will try a shorter timestep.
Best,
Nikola
On Sat, 2007-08-11 at 13:28 -0700, David A. Case wrote:
> 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 - 06:08:11 PDT
