[gmx-users] Implicit Solvent System - Energy Minimization

Mark Abraham Mark.Abraham at anu.edu.au
Thu Apr 16 03:31:08 CEST 2009

Grace Tang wrote:
> Sorry, I wasn't too clear in the first message.  I will be using OpenMM 
> Gromacs, which does support implicit solvent.  
> My current energy minimization steps only lower the energy to -5E3.  Is 
> this okay considering water is not around?


> Is is necessary to do equilibration if I am using implicit solvent?  

Yes. Generated velocities on an arbitrary starting structure will not 
necessarily be in the correct thermodynamic ensemble.

 > Is
> so, can anyone direct me to reasonable parameters?

Parameters for what? You should be looking closely at the documentation 
for OpenMM, and the methods in whatever publications they may have made 
using it. If they haven't published, and you aren't in close contact 
with them, then you should reconsider your choice of software. The kind 
of science you want to do should usually drive that choice.


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