[gmx-users] Re: Increase in charge after adding the ligand

[Mark Abraham]

On 21/06/2011 12:05 PM, bharat gupta wrote:
> Hi,
>
> Initially while preparing the structure , -2 charge was there on the 
> protein. Next, after adding the ligand and executing grompp statement 
> It showing -9.9 charge.

See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic, 
which may be relevant.

> So I added 9 sodium ions. but still its showing +8 charge on the 
> system. what shall I do in this case ??

-9.9 has been filtered through your head. We'd much rather see the 
output of your terminal, copied and pasted. There's no way that -9.9 
plus 9 sodium atoms gives +8. There must be a gap in your understanding 
somewhere, which is why we want to see actual input and output, not 
guesses and memories :-)

Mark