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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