[gmx-users] No addition of ions

Mark Abraham Mark.Abraham at anu.edu.au
Wed Sep 7 08:19:17 CEST 2011

On 7/09/2011 4:14 PM, aiswarya pawar wrote:
> Hi Gromacs users,
> Am running a MD simulation over a protein complex and before adding 
> the ions. we run a grompp option then we get result as model net 
> charge as some integer ie if +2.00. so we got to add 2 CL ions. But 
> when i ran my protein for grompp it didnt give me any net charge so am 
> not able to add any ions. is this correct??

There is no need to neutralize something that is already neutral. 
Whether it should be neutral is a function of your termini and side 
chains, and only you can address that. Whether you might want 
charge-balanced ions in your aqueous phase is also something for you to 


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