[gmx-users] Why so many energy minimization and position restrained simulation steps?

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Nov 20 09:18:41 CET 2007

Hi Peggy,

To understand the differencxes between the runs, you'll have to read and
compare the .mdp files well. I'd suggest to start with the Gromacs manual,
chapter 7. For one, position restraint MD depends on the presence of [
position_restraints ] in the topology and has nothing to do with the length
of the run. Please do some more background reading on MD. Often, inclusion
of the [ position_restraints ] is controlled in the .mdp file by adding a
define statement (-DPOSRES).

Why Bonvin uses so many steps of energy minimization and position restraint
MD is unclear to me. For a normal MD simulation it's not necessary. A fairly
common scheme used is:

1. EM in vacuum
2. EM in solvent
3. PR MD
4. NVT MD equilibration
5. NPT MD equilibration
6. Production run

You could have a look at the following tutorial rather than Bonvins:

Hope it helps,


On Nov 20, 2007 6:29 AM, Peggy Yao <peggy.yao at gmail.com> wrote:

> Hi,
> I am new to Gromacs. I am following this tutorial:
> http://www.nmr.chem.uu.nl/~abonvin/tutorials/MD-Data/index.html<http://www.nmr.chem.uu.nl/%7Eabonvin/tutorials/MD-Data/index.html>.
> My
> question is: why it has multiple steps of energy minimization and
> position restrained simulation? Is that a common practice? What's the
> key difference among these steps?
> Thanks!
> Peggy
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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