[gmx-users] simulation in vacuum

[Xavier Periole]

David is right! There are no FF that has been parametrized for vaccum
simulations and the best you can do is using a classical FF and neutralize
charges to avoid collapses ...

be aware of what you do ...

On Wed, 17 Sep 2008 19:13:33 +0200
  David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Thomas Schlesier 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.
> 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) 
>http://pubs.acs.org/cgi-bin/download.pl?bi061182y/B6CC.
> 
> 
> 
>> 
>>> > 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
>>> >
>>> > _______________________________________________
>>> > gmx-users mailing list    gmx-users at gromacs.org 
>>><mailto:gmx-users at gromacs.org>
>>> > http://www.gromacs.org/mailman/listinfo/gmx-users
>>> > Please search the archive at http://www.gromacs.org/search before posting!
>>> > Please don't post (un)subscribe requests to the list. Use the
>>> > www interface or send it to gmx-users-request at gromacs.org 
>>><mailto:gmx-users-request at gromacs.org>.
>>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> 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.
>> Thomas
>> 
>> 
>> ------------------------------------------------------------------------
>> 
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the 
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> -- 
> 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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface 
>or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-----------------------------------------------------
XAvier Periole - PhD

Molecular Dynamics Group / NMR and Computation
University of Groningen
The Netherlands
-----------------------------------------------------