Re: Potential Energy and RMS-Deviation Issues

From: David A. Case <>
Date: Thu 1 Aug 2002 09:25:57 -0700

On Thu, Aug 01, 2002, 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

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

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
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Received on Thu Aug 01 2002 - 09:25:57 PDT
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