[gmx-users] limit in reducing time step for integration

[Justin A. Lemkul]

María Paula Longinotti wrote:
> The oscilations in pressure are different, they are much bigger for an 
> integration time of  0.0001than for integration times of  0.001 or 0.0005.
> 

I wouldn't base any conclusion on pressure or the fluctuations therein.  These 
quantities are extremely sensitive to any small change.  As long as the averages 
converge to (statistically) the same value, then there is no problem.

http://www.gromacs.org/Documentation/Terminology/Pressure

The timestep is involved in determining the coupling strength, so if you fix 
tau_p and adjust dt, you will see differences.  See manual section 3.4.9.

-Justin

>  > Date: Thu, 28 Jul 2011 12:27:19 -0400
>  > From: jalemkul at vt.edu
>  > To: gmx-users at gromacs.org
>  > Subject: Re: [gmx-users] limit in reducing time step for integration
>  >
>  >
>  >
>  > María Paula Longinotti wrote:
>  > > Hi,
>  > >
>  > > I have been making some tests reducting the time step for the
>  > > integration with md in the grompp.mdp file and observed that obtained
>  > > results differ when the time step is 0.0001 from those obtained for 
> time
>  > > steps 0.0005 and 0.001.
>  > > Do you have any idea of which can be the problem?
>  >
>  > Can you please be more specific about the nature of the differences 
> you see?
>  >
>  > -Justin
>  >
>  > --
>  > ========================================
>  >
>  > Justin A. Lemkul
>  > Ph.D. Candidate
>  > ICTAS Doctoral Scholar
>  > MILES-IGERT Trainee
>  > Department of Biochemistry
>  > Virginia Tech
>  > Blacksburg, VA
>  > jalemkul[at]vt.edu | (540) 231-9080
>  > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>  >
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================