[gmx-users] removing waters from a peptide
spoel at xray.bmc.uu.se
Thu May 29 13:25:01 CEST 2003
On Thu, 2003-05-29 at 12:14, kia balali wrote:
> 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!
this is correct, normally (with the default values ) genbox takes away
enough water to do a normal simulation, but you can make a larger void
around a protein the way you are suggesting.
> 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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Dr. David van der Spoel, Dept. of Cell and Molecular Biology
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