[gmx-users] Adding second solvent

Juliette N. joojoojooon at gmail.com
Sat Apr 6 23:37:29 CEST 2013

Dear all,

I need to add 100 molecules of a second solvent to my polymer. I do this in
two solvation steps as below:

genbox -cp Solute.gro -ci Solvent1.gro -o solute-solvent1.gro -nmol 500

genbox -cp solute-solvent1.gro -ci Solvent2.gro -o solute-solvent1-solvent2.gro
-nmol 100

1- Is this the correct of adding two solvents to a solute? or This has to
be done in one step.

2- Does the box size (last line in gro) of solvent affect the final box
size of the solute-solvent1.gro? I mean do I need to keep size of Solvent1.gro
or Solvent2.gro as small as possible to avoid huge box for solute-solvent1.gro
or solute-solvent1-solvent2.gro?

3- In mdp file do I have to assign the uniform solution temperature to each
component or that is sufficient to have tc-grps             =  System  ?

Thanks for your comments,
Have a great weekend

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