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

Ragnarok sdf fabracht1 at gmail.com
Tue Feb 17 19:10:28 CET 2009

I have tried with decane, octane and CCl4. The three of them got me
the same problem, pressure scaling more than 1%. I have tried
increasing the tau_p value, cause that was one of the solutions given
in gmx user's list. That didn´t work out either. All my simulations
were carried out using ffgmx forcield. I think the problem is due to
using the wrong parameters in my input mdp files, but I don´t really
know which. That is why I asked about some tutorial or something more
especific about building protein boxes with apolar solvents. If I
could choose, I would prefer using octane box with ffgmx forcefield
cause I will eventually work with a lipid bilayer and will use such a
forcefield in my simulations.

2009/2/17 Vitaly Chaban <vvchaban at gmail.com>:
>>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

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