[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
More information about the gromacs.org_gmx-users
mailing list