[gmx-users] Adding second solvent

[Justin Lemkul]

On Sat, Apr 6, 2013 at 5:37 PM, Juliette N. <joojoojooon at gmail.com> wrote:

> 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.
>
>
It is not possible to use the -ci -nmol mechanism with multiple molecules
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?
>
>
Did your approach work? The box vectors in the inserted coordinate file are
irrelevant.


> 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  ?
>
>
Technically, coupling the system together is the only correct way to treat
thermostats. In practice, the exact implementation depends on the chosen
thermostat algorithm. See extensive discussions in the list archive on this
topic.

-Justin

-- 

========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================