[gmx-users] vdwd option on genbox: Exactly what does it do?

David van der Spoel spoel at xray.bmc.uu.se
Mon Jan 9 19:51:26 CET 2006

David Mobley wrote:
> Dear all,
> genbox has a -vdwd option which specifies "default vdwaals distance". 
> The documentation isn't too clear about this; does it override what 
> genbox usually uses? Or is it only used for molecules which have no vdW 
> parameters or some such?

> For anyone who cares: I'm trying to keep water somewhat further away 
> from the protein when solvating than is typical, and I'm trying to 
> figure out whether using -vdwd is a way to do this, or whether I'll have 
> to make a script to delete all of the waters within my desired cutoff 
> distance from the protein.
You want to copy the vdwradii.dat file to your working directory and 
edit that.
> Thanks,
> David
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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