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

[Vitaly Chaban]

>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.


Best,
Vitaly

-- 
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