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

Mark Abraham mark.j.abraham at gmail.com
Wed Jul 8 08:39:10 CEST 2015


Since you know how to add n molecules, and you want a solution with a given
molality, work out how many molecules that is, and then add that many
molecules. Decide whether you care about the volume excluded by the protein
when considering what that molality means.


On Wed, Jul 8, 2015 at 6:51 AM SAPNA BORAH <sapnauser365 at gmail.com> wrote:

> 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
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