Date: Thu, 1 Aug 2002 09:25:57 -0700
From: "David A. Case"
Subject: Re: Potential Energy and RMS-Deviation Issues

On Thu, Aug 01, 2002, mdk7p wrote:
>
> I ran a 1ns production over the course of 5 200ps runs on a triplex
> (no water, PME used, Zn2+ counterions, 1fs timestep, 300K, 5kcal DNA
> and 25 kcal ion restraints throughout the run). When I plotted the
> potential energy over the course of the calculation, it stayed steady
> throughout each individual run, and dropped ~100 kcal/mol between
> each restart. As a result, my graph looks like a set of stairs. Is
> this common, or did I foul up somewhere?

This should not happen. If you are unsure about restarts, try very short
tests. For example:

Do a 100-step run with ntpr=1
Do a second one, starting from the end of the first

Go back to the beginning and to a 200-step run from the original starting
point.

Compare your results. Generally the two should be identical...might be
the smallest amount of round-off error, but nothing like what you report.

Running a charged system with PME and no water is likely to lead to
considerable periodic artifacts, especially if your box is not very big.
If you have no waters, set ntb=0 (and consider turning on GB, but that's
probably a different issue.)

>
> Also, I ran a 1ns production over 5 200ps runs on a duplex in a
> waterbox (5500 waters, PME used, Zn2+ counterions, 2fs timestep,
> 300K, no restraints). The PE was fine in this case, but the RMS-
> deviation seemed to start at 0 and drift gradually up to 1-1.5A after
> each restart. Is this supposed to happen?
>

No. The fact that the RMS goes back to zero at each restart suggests you
are not really starting each new step from the end of the previous one(?).

..good luck...dac