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,
generally.
If you post your .mdp file, you may get some feedback on which settings might be
inappropriate.
-Justin
2009/2/17 Vitaly Chaban <[email protected]>:
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: [email protected]
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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