[gmx-users] Structure optimization failure

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 29 14:06:49 CEST 2012

On 6/29/12 8:04 AM, Lara Bunte wrote:
> Hi
> Thank you for the fast answer :-) I use a tip3p water model. I wrote spc216 because this is what I am using with genbox. My mistake.
> Now I used the equilibrating file out of this tutorial:
> http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html
> I got the same problem. The water could not be settled.
> What is wrong with this file for my system?

The settings in my tutorial are for use with OPLS-AA and are thus not suitable 
for a simulation with CHARMM.  Cutoffs and other aspects will be different.

You said your goal was energy minimization.  The script provided above is for 
equilibration after EM.  The tutorial also contains an EM script that is more 
suitable but will still likely require some small adjustments.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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