[gmx-users] Force Field for Vacuum simulation

James Starlight jmsstarlight at gmail.com
Sun Jan 29 15:29:27 CET 2012

Hi David!

Thanks for reference I'll study it carefully.

I have some general question about the vacuum simulation

1- I've found that common GROMOS fields are not suitable for the
vacuum simulation because of its implementation for condensed phase .
But In some referencces I've found that people use 53.6 ff for the in
vacuum simulation. In addition Ive done minimisation and equilibration
in that ff in vacuum and my system have not been collapse :) Is there
any wy to adopt this ff for the in vacum ?

2- I have uncommon onject for simulation. It's GFP protein where
chromophore group ( like ligand) is covalent bonded to the backbone of
this protein. As I've understood in Justins tutorial there are no any
covalent bonds between protein and ligand. But how I could make this
bond if I operate with TWO topology files ( one for chromophore and
another for protein itself) ? I've done all steps in accordance to
Justins tutorial but on the minimisation step my chromphore dissuse
out of the protein interior because of absent of backbone group.

Thanks again,


2012/1/28, David van der Spoel <spoel at xray.bmc.uu.se>:
> On 2012-01-29 07:20, James Starlight wrote:
>> Dear Gromacs USers!
>> I'm looking for good force field for the simulation of the
>> protein-ligand complex in vacuum.
>> In accordance to the Justin's tutorial I've found that GROMOS96 43b1
>> force field might be good choice for that task.
>> But my version of GROMACS lack for that force field .rtps :(
> Because that ff is not well-documented, the only difference with the
> normal gromos43 force field is that the side chains are neutral.
> Please check this paper for a comparison of FF for vacuum simulations:
> Erik Marklund, Daniel Larsson, Alexandra Patriksson, David van der Spoel
> & Carl Caleman: Structural stability of electrosprayed proteins:
> temperature and hydration effects Phys. Chem. Chem. Phys. 11 pp.
> 8069-8078 (2009)
>> Could you tell me where I could dwnload this force fields parameters?
>> Thanks,
>> James
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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