AMBER Archive (2009)

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

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Tue Oct 20 2009 - 19:39:22 CDT

> 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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