AMBER Archive (2005)

Subject: RE: Re: AMBER: a trivial question

From: Linchen Gong (glc0358_at_vip.sina.com)
Date: Fri Aug 05 2005 - 10:26:25 CDT

Dear Carlos:
     I think nstlim/ntwx is a approximate estimate. For my question I found that the first 100000 step breeds 1000 frames, however the subsequent 100000 step only produces 999 frames.Further more, things become more strange when computer crash occurs, e.g a process was crashed at 11ps, restarted from 10ps and crashed again at 111.4ps, 0.002ps per step ntwx=200, ntpr=100. The whole process brings 252 frames, but I think it ought to be more. It seems that amber doesn't write mdcrd file every ntwx steps, instead, it delays a little.
    This question is quite trivial, but I want to know the answer to avoid some potential analysis error.
    Thanks a lot!
----- Original Message -----
From:Carlos Simmerling <carlos_at_ilion.bio.sunysb.edu>
To:amber_at_scripps.edu
Subject:Re: AMBER: a trivial question
Date:Thu, 4 Aug 2005 19:28:36 +0800
> Linchen Gong wrote:
>
> >Dear amber users:
> > I have a trivial question that I do not understand. If I run a 100000 step MD simulation with a writing frequency to mdcrd file of 100, then howmany frames will the mdcrd contains?
> > If I run another MD simulation with the restrt file of the former one. the total number of step is also 100000 and mdcrd writing frequency is still 100, howmany frames will be there in the mdcrd file and why?
> > Since my computer shut down automaticly sometimes, I want to know the answer.
> > Thanks a lot
> >
> >
> >
> >
> divide nstlim by ntwx.
>
>
>
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______________________________________
Linchen Gong
basic science class
math and physics oriented
Department of physics
Tsinghua University
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