Re: AMBER: Is the MD simulation normal

From: Bill Ross <>
Date: Sat, 28 May 2005 10:00:42 -0700 (PDT)

> After the switch to NPT, the volme slow down quickly and soon reached
> the equilibration. It is normal.
> About you word " I apply restraints during the usual volume
> shrinkage",, do you mean that during the NPT, II should apply
> restraints after the NVT for some simulation time and the continue
> the NPT without restraints?
> The volume change as a function of time is attached. It seems normal.

It is probably normal for equilibrating a structure solvated
by leap's water placement algorithm (shrinkage by about 1/6
of the volume). However it is an artifact of the modeling
process, therefore I would keep the solute molecules fixed
in some way until volume has stabilized.

It is possible that the restructuring of the water and the scaling
of all the atoms toward the origin may have weakened the hbonds you
are interested in. However it is difficult to know, since the hbonds
broke some 200 ps after the shrinkage occurred. You could try graphing
the rms deviation from the fitted structure to see how long the NPT
equilibration phase lasted.

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Received on Sat May 28 2005 - 22:53:02 PDT
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