[gmx-users] potential energy =nan

[Sheyore Omovie]

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.
Meanwhile, I'll try Martin's advice on making the water flexible.
Rgds
John


>From: Mark Abraham <Mark.Abraham at anu.edu.au>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at 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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