[gmx-users] which vdwradii in pqr coming from editconf -mead ??

David van der Spoel spoel at xray.bmc.uu.se
Tue Aug 29 08:40:21 CEST 2006

pascal.baillod at epfl.ch wrote:
> Dear community,
> I am producing pqr files with editconf -mead (starting from tpr files) in order
> to process them with apbs. The charges are the same as those of my topology, but
> I can't figure out from where the van der Waals radii are coming:
> -They don't match the ones I found in the file share/gromacs/top/vdwradii.dat
> -They don't match the ones I compute starting with the C6 and C12 coefficients
> of the LJ potentials. I compute them with eps=(C12/C6)^(1/6). 
> Thank you very much for any hint!

there are different options:

        -rvdw   real   0.12  Default Van der Waals radius (in nm) if one can
                             not be found in the database or if no 
                             are present in the topology file
       -sig56   real      0  Use rmin/2 (minimum in the Van der Waals
                             potential) rather than sigma/2
-[no]vdwread   bool     no  Read the Van der Waals radii from the file
                             vdwradii.dat rather than computing the radii
                             based on the force field

Default is to compute them from the lennard jones parameters. Note that 
if you want to reproduce literature data you need to use their charges 
and radii.

By the way, we have tried some calculations with MEAD, but find that the 
results are chaotic. An infinitesimal change in coordinates will give 
very large variations in energy, and there is no convergence to a 
certain energy if one makes the grid spacing smaller either. Is that a 
generic feature of these kind of programs? Is it better in APBS?

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://folding.bmc.uu.se

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