[gmx-users] how to make 8M solutions??
sapnauser365 at gmail.com
Fri Jul 10 05:53:42 CEST 2015
Sapna Mayuri Borah
c/o Dr. A. N. Jha
On Wed, Jul 8, 2015 at 12:08 PM, Mark Abraham <mark.j.abraham at gmail.com>
> 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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