[gmx-users] solvent molecules between....another question...
acorrea at unisa.it
acorrea at unisa.it
Wed May 11 14:00:18 CEST 2005
Hallo to everybody.
I have another question close to this of Marc
I would like to do a rdf analysis of the solute-solvent molecules(benzene)
between two ions. Is there a tool in gromacs that does it?
bye bye and thanks in any case
Scrive Anton Feenstra <feenstra at few.vu.nl>:
> Marc F. Lensink wrote:
> > On Mon, Apr 18, 2005 at 03:54:45PM +0530, Alok wrote:
> >>hello gromax users,
> >> I have simulated a protein-peptide
> >>complex solvated in water.
> >>Now i want to specifically analyse the number of solvent molecules
> >>between the protein-peptide complex as a function of time.
> >>Is there any direct or indirect tool available in GROMACS to help me
> >>carry out this analysis.
> >>Please suggest some solution.
> >>Thanking you all in advance.
> > i have a tool that may do what you want. i've used it for
> > peptide/lipid interaction, to define the lipids that are under the
> > peptide. as in a membrane simulation the normal to the bilayer is
> > typically the z-axis, you'll have to rotate your system to conform to
> > this convention. i think you can do that by using editconf to
> > generate one such structure, and then with trjconv you fit all frames
> > to that reference structure. contact me off-list if you want to get
> > the source of the program.
> You may as well get around by using g_hbond. Although it is desinged for
> H-bond detection, it could easily be modified (in the source code, that
> is) to look at any type of close contacts.
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