[gmx-users] Ionization with different ions of different concentrations

[Justin Lemkul]

On 9/6/19 12:45 PM, Mohammed I Sorour wrote:
> Dear Gromacs users,
>
> I'm trying to add MgCl2 (100 mM) and NaCl (6 mM) to my system which has
> (-22 net charge).
>
> I add a neutralizing amount of Mg or Na using the genion  neutral option.
>
> But when it comes to the salt concentration, I'm failing to have both of
> the salts added simultaneously. Like it will let me add Mgcl2 or Nacl.
>
> I use the following command:
> gmx genion -s ions.tpr -o sys_solv_ions.gro -p topol.top -pname MG -pq 2
> -nname CL -conc 0.1 -neutral
>
> If I try to add Na and Mg at the same time:
> gmx genion -s ions.tpr -o sys_solv_ions.gro -p topol.top -pname MG -pq 2
> -np 51 -nname CL -nn 82 -pname NA -np 2
>
> I get the following message, which makes sense:
>
> Error in user input:
> Invalid command-line options
>    In command-line option -pname
>      Option specified multiple times
>    In command-line option -np
>      Option specified multiple times
>
>
> So my question is
> 1-Can we neutralize the system with different ions. like in my case (10 Na
> ions and 6 Mg ions)?

Not automatically or in one command.

> 2-How can we add different salts with different concentrations?

Manually specify how many of the first ion you want to add with -pname 
-pq -np, update your topology, make a new .tpr file, and add the second 
ion in the same way.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
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jalemkul at vt.edu | (540) 231-3129
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