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

[SAPNA BORAH]

Dear all,

I am trying to add gdmcl to a protein, however I am unable to make molal
solutions.
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.


Regards,
Sapna

Sapna Mayuri Borah
Research student
Tezpur University,
India