[gmx-users] Force Field for Vacuum simulation

Justin A. Lemkul jalemkul at vt.edu
Sun Jan 29 15:35:24 CET 2012

James Starlight wrote:
> 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.

The GFP chromophore is part of the backbone of the protein, is it not?

The tutorial I have for a protein-ligand complex should not be taken to mean 
that all non-protein entities are physically separate entities.  Plenty of 
cofactors, chromophores, and the like are covalently attached to the protein.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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