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

Justin A. Lemkul jalemkul at vt.edu
Tue Feb 17 19:14:45 CET 2009

Ragnarok sdf wrote:
> 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.

I think what you were asking for was too specific.  "Building protein boxes with 
apolar solvents" is hardly different from building a normal protein simulation 
system in water.  The difference comes with what parameters you use for the 
solvent and what you specify in your .mdp file.  The molecule parameters have to 
be verified appropriately, and the .mdp settings come from the literature, 

If you post your .mdp file, you may get some feedback on which settings might be 


> 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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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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