AMBER Archive (2005)

Subject: RE: RE: Re: AMBER: a trivial question

From: Linchen Gong (glc0358_at_vip.sina.com)
Date: Fri Aug 05 2005 - 21:52:39 CDT

Dear Davis:
     Hello, Thank you for your help:) I will check it.

> Dear Linchen,
>
> I am not sure if this will help your problem, but this is my experience
> nonetheless:
>
> We are have two clusters, one is a cluster of Compaq Alphas and one is a
> cluser of 64-bit AMD opterons, and both run Amber 8. For some reason,
> the Alpha cluster will update the mdcrd file automatically at the
> expected interval, but the opterons are different. For some reason, the
> opterons must fill a memory buffer first, and once this buffer is full
> of data (like that made for the the mdcrd file) only then will it write
> to the file. This means that there is some lag or delay to writing to
> the mdcrd file. Also this unfortunately means that if some power outage
> or computer failure occurs, then the mdcrd file is always missing the
> most recent data (that mdinfo will report because its opened and closed
> every time). The problem is not isolated to Amber either, as the same
> functionality can be seen with DL_POLY and many other programs.
>
> To find what you indeed have in your trajectory file, you can always use
> ptraj's trajin/trajout function. At the end of the ptraj run it outputs
> the number of saved configurations to the screen so you no longer have
> to guess.
>
> Hope this helps,
>
> David LeBard
> Dept of Chemistry and Biochemistry
> Arizona State University
>
> On Fri, 2005-08-05 at 08:26, Linchen Gong wrote:
> > 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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>

______________________________________
Linchen Gong
basic science class
math and physics oriented
Department of physics
Tsinghua University
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