[gmx-users] How to use the dummy atom?

PeiQuan Chen gromacs at 163.com
Tue May 20 14:57:01 CEST 2003

Dear gmx-users:
   Recently I want to do the free energy calculations about the cyclodextrin with 
    Ph-C-OH. The latter molecule can adopt two stereoisomers, designated as R. and S.
I want to use Gromos force field , which use unite atom. So the molecule can represent as
    Ph-C-OH.       (R.S)
       Dummy atom

I want to know how to use Dummy atom to represent the molecule.
   Can anyboby give me some hints to how the creat the latter molecular top files? Because I haven't 
any experience on use the dummy atoms, I wish you can give me a example top file for it. 
  Thank you in advances.
Sincerely yours
PeiQuan Chen
PeiQuan Chen 	Department of Chemistry, Nankai University
WeiJin Road 94, TianJin, 300071, P.R.China
phone:	(86)2223506728		Mobile Phone: (+86)13920675030
gromacs at 163.com	

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