[gmx-users] about counterions

Rui Li moonfine at mail.sdu.edu.cn
Tue May 15 04:57:38 CEST 2007

Dear Mark

Thank you for your reply

Do you mean I can ignore the charge?
If the topology is broken, what should I do? 

>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] about counterions
>Date:Tue, 15 May 2007 00:10:01 +1000
>Rui Li wrote:
> > Dear all,
> > I am new to gmx.
> > When I run grompp, it prompt:
> > System has non-zero total charge: 1.172000e+01
> > 
> > The number isn't integer, So how many counterions I should add?
> Never mind about ions, probably your topology is broken before you got 
> started :-) Check your capping groups. If you used pdb2gmx, have a look 
> at the right hand (comment) column of the atom listing, where it shows 
> the cumulative charge. This will help you find the residue where things 
> start getting non-integral.
> Mark
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