[gmx-users] removing waters from a peptide

[David]

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
> 
> Kia Balali-Mood
> Dept. of preclinical Veterinary Sciences
> Laboratory of Membrane Biophysics
> The Vet School
> College of Medicine & Veterinary Medicine
> University of Edinburgh
> Summerhall
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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