[gmx-users] Re: RE: logfile size

[lloyd riggs]

-------- Original-Nachricht --------
> Datum: Wed,  7 Dec 2011 12:00:05 +0100 (CET)
> Von: gmx-users-request at gromacs.org
> An: gmx-users at gromacs.org
> Betreff: gmx-users Digest, Vol 92, Issue 34

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> Today's Topics:
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>    1. Re: RE: logfile size (Mark Abraham)
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> ----------------------------------------------------------------------
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> Message: 1
> Date: Wed, 07 Dec 2011 20:15:17 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] RE: logfile size
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4EDF2EA5.5020803 at anu.edu.au>
> Content-Type: text/plain; charset=UTF-8; format=flowed
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> On 7/12/2011 7:41 PM, lloyd riggs wrote:
> > Message: 3
> > Date: Tue, 06 Dec 2011 18:58:50 +0100
> > From: Javier Cerezo<jcb1 at um.es>
> > Subject: Re: [gmx-users] RE: logfile size
> > To: Discussion list for GROMACS users<gmx-users at gromacs.org>
> > Message-ID:<4EDE57DA.80405 at um.es>
> > Content-Type: text/plain; charset=UTF-8; format=flowed
> >
> > Not the main problem, but your dt=0.0002 (0.2fs), is it what you want?
> >
> > Javier
> >
> >
> > Yeah,
> >
> > I found when you have 10,000 + protein atoms + assorted others (2
> different ligands of say 5000K atoms) the time steps have to remain smaller or
> you start getting problems with all sorts of things from Temp coupling to
> simple integrations between steps.  I can EQ it at 0.02, for 1M steps or more,
> and still run into the same problem when I switch to MD integrators.  Dont
> know if this is universal though, as I spent time making sure the models
> are correct, ie error free after EQ's (em, NVT, NPT).  They run though fine
> at that time step, it just makes the whole simulation take a while to run,
> as time steps translate into direct computational time.
> >
> 
> Post-equilibration MD at normal T and P with all bonds constrained 
> should be stable with 2fs time steps. If not, then I'd say there's 
> something wrong with the parameters and a smaller time step is not 
> actually a fix.
> 
> Mark
> 
> 
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Dear Dr. Abrahams,

Your right, I can if I look overthings get it to run at that time step, which I should do.  I origionally had to lower it that much in intitial eq's, but added an extra zero in somewhere, and then moved on to mass production schemes.  Thus, I am wasting some of my own time, but will change it for the next set of runs just to make sure.

Thanks,

Stephan Watkins

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