[gmx-users] Ionization: Your solvent group size (76663) is not a multiple of 3
jalemkul at vt.edu
Mon Sep 23 12:45:08 CEST 2019
On 9/16/19 11:41 AM, Mohammed I Sorour wrote:
> Dear Gromacs users,
> I'm adding two different salts to my system in different concentrations;
> first salt addition is done successfully using the following commands:
>> gmx grompp -f em.mdp -c sys_solv.gro -p topol.top -o ions.tpr
>> gmx genion -s ions.tpr -o sys_solv_ions.gro -p topol.top -pname MG -pq 2
> -nname CL -conc 0.1 -neutral
> For the second salt, I generated a new tpr file and used the
> following commands:
>> gmx grompp -f em.mdp -c sys_solv_ions.gro -p topol.top -o ions2.tpr
> gmx genion -s ions2.tpr -o sys_solv_ions.gro -p topol.top -pname NA -nname
> CL -conc 0.006
Is this really the intended concentration, 6 mM? You will need an
enormous box to add more than a single ion here.
> But for the second salt addition, I get a fatal error.
> Selected 4: 'SOL'
> Program: gmx genion, version 2016.3
> Source file: src/gromacs/gmxana/gmx_genion.cpp (line 500)
> *Fatal error:Your solvent group size (76663) is not a multiple of 3*
> Any hints about this issue? Also, why should the solvent group size
> multiple of another number? Like, I have seen the case with other gromacs
It's a sanity check. If you're using a 3-point water model, and your
chosen solvent group is not an integer multiple of 3, something is wrong
with it. Check your topology and coordinates after the first addition
you did, and make sure you chose the correct group for replacement,
because something is broken.
Justin A. Lemkul, Ph.D.
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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