[gmx-users] removing waters from a peptide

kia balali kiabalali50 at hotmail.com
Thu May 29 12:15:02 CEST 2003

Hi Mojtaba,

If u go into usr/local/share/gromacs/top or whatever the path is for where 
the vdwradii.dat file is located and change the vdw radius of atoms present 
in your peptide....you can do this for up to 0.4 nm..before you start 
simulating..I've used this method for bilayers as well!

Dear Drs. Van der Spoel, Lindah, Feenstra etc...please correct me if I'm 
wrong in suggesting this method!


Kia Balali-Mood
Dept. of preclinical Veterinary Sciences
Laboratory of Membrane Biophysics
The Vet School
College of Medicine & Veterinary Medicine
University of Edinburgh

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