[gmx-users] RE: Help with apolar solvent box

Vitaly Chaban vvchaban at gmail.com
Tue Feb 17 16:53:49 CET 2009

>Hello, I would like to know if there is any recommendation onto
>setting up a system with a protein in a apolar solvent box. If there
>is any tutorial or web page with topologies for solvents. I read that
>the decane box that comes with gromacs is not to be used for
>simulations, if that is true, then how should I assemble my system?

Hi Fabrício,

It seems nothing is extremely specific in your task if the force field
is ready. What solvent do you need? Is it really decane? I have never
worked with decane topology provided with gromacs but I know there's
some well-studied ones in the literature.
Read about editconf and genbox standard gromacs utilities to make your box.


Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua
skype: vvchaban

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