[gmx-users] how to make 8M solutions??

SAPNA BORAH sapnauser365 at gmail.com
Wed Jul 8 06:51:12 CEST 2015

Dear all,

I am trying to add gdmcl to a protein, however I am unable to make molal
I can add gdmcl by -nmol command but to make molal solutions is giving me a
hard time. This is a basic query but it has been bugging me for quite a
long time.

Please put some light on doing this...

I have been using the following commands to make the gdmcl box:

editconf -f mod.pdb -bt cubic -d 0.1 -box 5 5 5 -o box.gro
genbox -cp box.gro -ci file_1.pdb -p topol.top -o guan.pdb -nmol 100

editconf -f guan.pdb -bt cubic -d 1.2 -o box_2.gro
genbox -cp box_2.gro -cs spc216.gro -p topol.top -o solvated.gro

The simulations I have been running well with the included 100 GdmCl,
however, the problem with making the molal solutions still remains.


Sapna Mayuri Borah
Research student
Tezpur University,

More information about the gromacs.org_gmx-users mailing list