AMBER Archive (2009)

Subject: Re: [AMBER] amber8 pmemd trajectory coordinates problem

From: Sergio Wong (wong105_at_llnl.gov)
Date: Tue Oct 20 2009 - 19:49:11 CDT

Hi;

     Thanks for the note. I think I should have said, every 4th
SAVED trajectory step so that every 20,000, 1fs steps, is when the
coordinates seem to move forward more than the previous 3.

Thanks.
-Sergio
At 05:39 PM 10/20/2009, you wrote:

> > I ran an explicit water simulation (TIP3P, PBC, counter ions,
> > pme, etc) using PMEMD version 8. The problem is that when I visualize
> > the trajectory it seems to advance very little except every 4th
> > trajectory step. The system is of medium size ( 48732 Atoms) and my
> > input file is below:
>...
>
> > nrespa=4,
>
>If this problem is every 4th step, likely the NRESPA is the culprit.
>
>
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