[Fwd: Re[2]: [gmx-users] dummy particles]

[David van der Spoel]

On Fri, 2004-11-12 at 09:01 +0100, David van der Spoel wrote:
> -------- Forwarded Message --------
> From: Arturas <a3arzi at vaidila.vdu.lt>
> Reply-To: Arturas <a3arzi at vaidila.vdu.lt>
> To: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re[2]: [gmx-users] dummy particles
> Date: Fri, 12 Nov 2004 09:37:02 +0200
> Hi,
> 
> It's a thianizol molecule with pro-chiral electron lone pairs on
> sulfur atom. However, in enentioselective catalysis there is a metter
> which pro-chiral lone pair of sulfur will be attacked during
> reactions.
> 
> I want to calculate various distances between 'lone pairs', which
> would be replaced by dummy or other particle (atom), and other atoms
> in my system in my simulations.
> 
>       pro-S_l.p                 X1
>       |                         |
> Phen.-S-CH3        -->>>  Phen.-S-CH3
>       |                         |
>       pro-R_l.p                 X2
> 
> The problem is that I didn't found the apropriate dummy constraction
> type from manual for my problem.

Check the topology for TIP5P, if they are out of the plane, if they are
all in one plane you define the S position to be the dummy and use
impropers to keep the other four atoms in the plane.
> 
> Could I introduce an atoms, e.g. X, with zero charge, zero constants
> and constrained X-S distance ? Would it solve my needs ?
> 
> Arturas
> 
> |----->
> >> I want simulate a sulfide with bounded particles (dummy atoms) at the
> >> position of lone pairs of sulfur in order to evalute ONLY the
> >> structural information of that 'lone pair' paricles in my trajectory.
> >> 
> >> According manual all dummies are computed as functions of other atoms.
> >> But i didn't found any appropriate dummy construction type to my
> >> problem. The main problem that these lone pairs are not plain so i can
> >> not use 2, 3, 3fd, 4fd.  Maybe i'm wrog ?
> >> 
> >> Can anyone give a piece of advise how to treat such a 'position
> >> markers' ?
> 
> DvdS> Please give more information on the chemistry of your molecule.
> <-----|
> 
-- 
David van der Spoel <spoel at xray.bmc.uu.se>