[gmx-users] simulation in vacuum

[Justin A. Lemkul]

Xavier Periole wrote:
> On Wed, 17 Sep 2008 16:14:08 +0200
>  Thomas Schlesier <schlesi at uni-mainz.de> wrote:
>>> / Thank you.
>> />/ But i have one last question:
>> />/For epsilon_rf i use the relative permittivity of the medium. I 
>> simulate in />/vacuum so epsilon_rf would be 1?
>> /GROMOS ff is not parameterized for vaccum simulations of the b-something
>> version ... have look at the paper.
>>
>>
>> So i should use ffG43b1 instead of the other GROMOS96 force fields?
> That would be the right choice for the GROMOS43 ff series.

If I recall a previous discussion (somewhere in the archive), ffG43b1 is not 
actually a "vacuum" force field, but rather one where all of the titratable 
groups are in their neutral forms.

As for whether or not that is applicable to a vacuum simulation, I guess you'll 
have to decide.

-Justin

>> In the GROMACS manual i found that the cut-off-distance must at least 
>> be 1.4 nm for the GROMOS96 force field.
> Never believe what is written in a manual :))
> It is always better to keep the values that are used for parameterization
> (the one I gave you) when using a force field. The idea that bigger = 
> better
> does not work ... you change the balance of forces and thus the properties
> of the force field.
>> So can i use: type = cut-off; rlist = 1.4 and r_x = 1.7?
>> (the problem is that the only reference i find for ffG43b1 is the 
>> GROMOS manual, and that's not free avaible)
> Any paper from van Gunsteren group or Alan Mark groujp (GROMOS developers)
> would describe the simulation setup: no need of the manual for this.
>> Thanks for an answer
>> Thomas
>>
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> 
> -----------------------------------------------------
> XAvier Periole - PhD
> 
> Molecular Dynamics Group / NMR and Computation
> University of Groningen
> The Netherlands
> -----------------------------------------------------
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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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