AMBER Archive (2005)

Subject: Re: AMBER: Is the MD simulation normal

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Fri May 27 2005 - 13:14:30 CDT

> For the MD details:
> Several- stage constraints minimizations were performed first and then
> 50 ps NVT MD to heat up the system from 0 K to 300k was performed.
> During the constraints, I just only let the hydrogen free and at the
> NVT MD stage, the constraints force was 5 kcal/mol. After above, the
> following 1 ns NPT MD without any constraints was carried out.

What degree of volume change happened after the switch to
NPT? When did you lose the desired hbonds relative to the
volume equilibrating? If the hbonds were lost long after
the volume equilibrated, it's not such an issue, but in any
case I would apply restraints during the usual volume shrinkage.

Bill
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