[gmx-users] about counterions

Mark Abraham Mark.Abraham at anu.edu.au
Tue May 15 05:32:54 CEST 2007

Rui Li wrote:
> Dear Mark
> Thank you for your reply
> Do you mean I can ignore the charge?

Only if you want an expensive random number generator.

> If the topology is broken, what should I do? 

I already answered this. Appearing not to read the detailed reply that 
someone gave up their time to write, is a great way to avoid getting 
yourself any help in the future. :-)

>>> 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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