[gmx-users] g_rotacf

[David]

On Thu, 2004-02-26 at 22:55, Ilya Chorny wrote:
> Hi David,
> 
> trjorder will only allow me to perform the calulation of a certain number 
> of water molecules. The problem is that I don't know how many water 
> molecules are in the first solvation of my solute at each time point.
> I can estimate from the RDF but it would be much  easier just to give 
> a distance criteria. I will attempt to write my own analysis using the 
> template you provide.
> 
For the first shell it is quite easy, as you say you make an educated
guess and do it only for those molecules. The problem is of course
diffusion. The correlation function may be quite long lived, however, as
soon as the water moves out of coordination the correlation is gone...

> Thanks
> 
> Ilya
> 
> 
>  
> Thu, 26 Feb 2004, David van der Spoel wrote:
> 
> > On Thu, 2004-02-26 at 08:05, Ilya Chorny wrote:
> > > I want to see if the water molecules rotate faster or slower in the
> > > first solvation shell of my solute.
> > then you have to do it in two steps with trjorder first. g_rotacf does
> > not know about these things.
> > > 
> > > Ilya
> > > 
> > > 
> > > -----Original Message-----
> > > From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]
> > > On Behalf Of David
> > > Sent: Wednesday, February 25, 2004 10:36 AM
> > > To: gmx-users at gromacs.org
> > > Subject: Re: [gmx-users] g_rotacf
> > > 
> > > On Wed, 2004-02-25 at 19:42, Ilya Chorny wrote:
> > > > Hello,
> > > > 
> > > > I would like to add a -shell option to g_rotacf. Can anyone provide me
> > > > with a starting point?
> > > > 
> > > what do you mean? g_rotacf computes rotational correlation for molecules
> > > > Thanks
> > > > 
> > > > Ilya
> > > > 
> > > > 
> > > > 
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> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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