[gmx-users] Langevin dynamics
feenstra at chem.vu.nl
Mon Aug 4 08:47:01 CEST 2003
Alan Wilter Sousa da Silva wrote:
> 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.
No, combination of LD and MD is not implemented. Seeing that a QM/MM
approach has been implemented (partially, and not nearly release-ready,
and not by me), it may be an idea to have something like 'integrator'
groups, where arbitrary selections of molecules could be handled by
different integrators (i.e., MD, LD, QM, whatever). There does need to
be some arrangement for the border area between integrators, though.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" |
| | (Red Hot Chili Peppers) |
More information about the gromacs.org_gmx-users