Sheyore Omovie wrote:
Hi Mark,
I'm sorry, I assume you'll understand that I've carried out all the
steps before an EM run.
David said is because the coordinates are on top of each other, I'll
appreciate any more specific advice on how to fix this.
use a molecule viewer
Meanwhile, I'll try Martin's advice on making the water flexible.
Rgds
John
From: Mark Abraham <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Subject: Re: [gmx-users] potential energy =nan
Date: Wed, 20 Jun 2007 23:09:03 +1000
Sheyore Omovie wrote:
I am doing an Energy Minimisation run for two polypeptides in a box.
I get the range checking error, variable ci= .... and the simulation
crashes. After changing ns_type to simple, the simulation is running,
but very slowly and the first few steps return Epot=nan.
What could I have done wrong?
It's hard to tell from your description, since an energy minimization
is not a simulation... but please try following this general scheme
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation
Mark
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________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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