Re: fep

From: Chris Chipot (
Date: Sat Jul 16 2005 - 04:48:02 CDT


The case example of ethane ? ethane is rather straightforward. This
is a pseudo-propane molecule:

  H H H H
  | | |/
 /| | |

The central carbon is connected to both a CH3 and a H, on each side.
If you build a propane molecule, your only worry is to place the
extra H on each side. The easiest way is to use, as a rough guess,
the same coordinates as the carbon atoms of the two CH3 moieties
and let the energy minimization do the rest.

Since the ensemble of green atoms is excluded from the list of red
atoms (alternate topologies) and the relevant internal parameters
have been removed, there won't be any spurious clashes.

Chris Chipot

Chris Chipot, Ph.D.
Equipe de dynamique des assemblages membranaires
Unité mixte de recherche CNRS/UHP No 7565
Université Henri Poincaré - Nancy 1 Phone: (33) 3-83-68-40-97
B.P. 239 Fax: (33) 3-83-68-43-87
54506 Vandoeuvre-lès-Nancy Cedex


      To sin by silence when we should protest makes cowards out of men
                                                    Ella Wheeler Wilcox

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