[gmx-users] Langevin dynamics
Alan Wilter Sousa da Silva
alan at biof.ufrj.br
Fri Aug 1 14:00:01 CEST 2003
I used LD but not in GMX. The idea I employed is something like that:
A had a protein complexed with a substrate. I want solvent, but my
box system created is very big. So, I take a sphere embracing my whole
protein system with all solvent that can fit in and apply LD to a spheric
section region, lessing a smaller interior sphere under classic MD.
Moreover, the atoms under LD must be position restrained. Then, all
atoms outside the exterior sphere are removed.
I don't know if GMX is able to do it, since it will involve a radical
modification in topologies files.
See reference below for further details:
Stochastic molecular dynamics of peanut lectin PNA complex with T-antigen
Caffarena ER, Grigera JR, Bisch PM
JOURNAL OF MOLECULAR GRAPHICS & MODELLING 21 (3): 227-240 DEC 2002
On Thu, 31 Jul 2003, Anton Feenstra wrote:
> Jia-Lin Lo wrote:
> > Hi;
> > I would like to know how do you perform LD with not explicit solvent.
> > Did gromacs provide implict solvent model? If not, how did you simulate
> > the protein with LD method. How did you make gro and top files.
> > Thanks in advance.
> I never used LD, but Berk Hess (my roommate then, reads this list too) did.
> AFAIR, he only used distance dependent dielectric. There are rumours
> about an implicit solvent model bein implemented in Vijay Pande's group
> (Stanford U, for the folding at home project), but AFAIK it hasn't been
> released (yet).
Alan Wilter S. da Silva
Laboratório de Física Biológica
Instituto de Biofísica Carlos Chagas Filho
Universidade do Brasil/UFRJ
Rio de Janeiro, Brasil
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