[gmx-users] energy minimization settings

Kai Zhuang kai.zhuang at gmail.com
Mon Jul 11 18:15:25 CEST 2005

position restrained water decreases the degree of freedom (because
bonds dont change length), so you're only considering the position of
each water molecules instead of position of each individual atoms.

generally for EM you use set constraint = none, and use flexible
water.  you have to change the top file yourself to include a flexible
water topology.  (check past mails for the script) if you dont use
flexible water, system will likely reach machine precision without
reaching minimization goal very quickly.

steep is faster, but less accurate, as per described in the manual.
use steep first, if it's obvious it's not working, use cg + steep.

On 7/9/05, Lei Zhou <zhoumadison at gmail.com> wrote:
> Dear gmx-users,
> I am doing a simulation with a protein-ligand system. According to
> standard protocol, there should be energy minimization (EM) steps
> before and after adding ions. Should I do positional restrain on
> protein-ligand (put define= -DPOSRES into em.mdp file), or just use
> flexible water (put define= -DFLEXIBLE into em.mdp file, with
> positional restainr) during both
> EM steps? If I don't restrain the position of protein-ligand, will the
> EM change the starting structure?
> Should I set constraints on all-bonds during EM?
> I saw some people using flexible water here. What is the reason for that?
> For the two EMs, should I use steep for both or use steep + cg?
> Thanks in advance.
> Lei Zhou
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Kai Zhuang
BioMedical Engineering @ University of Toronto
kai dot zhuang at gmail dot com
kai.zhuang at gmail.com

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