[gmx-users] the value of nsteps in the mdp file in the on-line tutorial

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Apr 11 21:38:51 CEST 2012

Hey ;)

For those, you really have to consider what the purpoase of the
simulations is. For energy minimization it's getting rid of clashes
that might cause the system to blow up. For NVT equilibration the aim
is equilibrating the temperature, which is usually fast enough. For
NpT it's equilibrating the pressure, which may take a bit more time,
mainly because it fluctuates so wildly. Especially when aiming to do
later simulations with parrinello-rahman pressure coupling, NpT
equilibration requires a bit of care, and a Berendsen manostat. It's
true that larger system take longer to relax, but the relaxation for
these steps is fast enough anyway. The real trouble starts when
equilibrating under production simulation conditions. There the size
of the system is quite an issue, and relaxation times are usually
(much) longer than you care for.



On Wed, Apr 11, 2012 at 8:59 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> Acoot Brett wrote:
>> In the on-line tutorial of *Justin Lemkul
>> *(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html)
>> for both lysozyme, for the mini.mdp, nvt.mdp and npt.mdp, the nsteps =
>> 50000. Do you think this valus is depend or independent of the molecular
>> weight of the protein or not?
> The length of the simulation depends on the amount of time needed for the
> system to achieve whatever level of convergence is desired.  System size can
> play into this calculation, but I have never found it to be a significant
> factor.
> -Justin
> --
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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