[gmx-users] simulation in vacuum
David van der Spoel
spoel at xray.bmc.uu.se
Wed Sep 17 19:13:33 CEST 2008
Thomas Schlesier wrote:
>>> >>/ Thank you.
>> > />/ But i have one last question:
>> > />/For epsilon_rf i use the relative permittivity of the medium. I simulate
>> > />/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.
AFAIK the only difference between vacuum force field and normal force
field in GROMOS is the protonation state of the side-chains (please
check that this is still correct in the current force fields). For
vacuum simulations of relatively small proteins I would recommend using
no cut-off at all. Since there is no direct experimental information
about protein structure in vacuum, there is no reason to use the
solution values of the cut-offs. Without the shielding of the water
everything is different. Another interesting problem is to determine
which residues to protonate in the gas phase, see e.g. Patriksson et al.
Biochemistry 46 pp. 933-945 (2007)
>> > 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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> I looked in some older papers but found no values for epsilon_r and _rf.
> From older posts of this mailing list I got the impression that
> epsilon_r = 1 and epsilon_rf the value of the relative permitivity of
> the medium. In the case of a simulation in vacuum epsilon_rf would be
> also 1 and then I have no correction from the reaction field, also
> grompp tells me that epsilon_r = epsilon_rf would be meaningless with a
> reaction field. So I'm puzzeld.
> If both epsilon values have the same value, is it then equal to normal
> cut-offs (type = cut-off)?
> Sorry for the many questions.
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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