[gmx-users] potential energy =nan

[David van der Spoel]

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 <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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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