[gmx-users] solvent molecules between....another question...

[acorrea at unisa.it]

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 
andrea  
 
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. 
>  
>  
> --  
> Groetjes, 
>  
> Anton 
>  
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