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

Mohammed I Sorour Mohammed.Sorour at temple.edu
Fri Sep 6 18:45:21 CEST 2019


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

Thanks,
Mohammed


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