[gmx-users] genbox -ci solute.gro -nmol N

[Justin A. Lemkul]

Chih-Ying Lin wrote:
> 
> 
> Hi
> 
> Originally, in the topol.top file =>
> [molecule]
> solute 1
> 
> 
> After the command:
> genbox -cp one_solute.gro  -cs  spc216.gro -ci one_solute.gro  -nmol  N 
> -p topol.top
> in the topol.top file =>
> 
> [molecule]
> solute 1
> solvent 5000
> 
> I think the flag "-p topol.top" in the genbox command did not do it 
> correctly.
> I am considering the two possible modification on the topol.top file
> [molecule]
> solute (1+N)
> solvent 5000
> 
> 
> [molecule]
> solute (1+N)
> solvent (5000 - N)
> 
> Which one is correct?

Depends, what's in the genbox output structure?

> Or, none of them is correct?
> What is the correct form of it?
> 

It is often easier to insert a molecule with -ci, then solvate in the next step 
(at least from a conceptual standpoint).  I don't know how the code will handle 
it, but it should certainly clear up your confusion.

-Justin

> 
> Thank you
> Lin
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
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-- 
========================================

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

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