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

David van der Spoel spoel at xray.bmc.uu.se
Fri Nov 12 09:01:43 CET 2004

-------- 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

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

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.

Could I introduce an atoms, e.g. X, with zero charge, zero constants
and constrained X-S distance ? Would it solve my needs ?


>> 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>

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