AMBER Archive (2002)

Subject: Re: Potential Energy and RMS-Deviation Issues

From: CUI, Guanglei (cuigl_at_morita.chem.sunysb.edu)
Date: Thu Aug 01 2002 - 10:38:36 CDT

Hi,
    This is my guess since I don't know how you did the 5 runs. But if
    you did them consecutively (always restart from the previous one),
    you may check your input and see if you used irest = 1. If not, you
    may try to repeat with this setting.

On Thu, 1 Aug 2002 mdk7p_at_cms.mail.virginia.edu wrote:

> Hello everyone,
>
> I am analyzing a few recent MD runs, and I've come across a few
> strange results that I wanted to get some advice on from the pros.
>
> 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?
>
> 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?
>
> Thanks!!
>
> Best,
>
> Mike Keller
> UVA Chemistry Dept.
>
> 

-- 
Guanglei Cui
Dept. of Chemistry
SUNY at Stony Brook
Stony Brook, NY 11790