[gmx-users] Solvent-accessible volume and other quantities for comparison with experiment

[David]

On Tue, 2005-08-09 at 19:59 +0200, Steven Kirk wrote:
> Hello,
> 
> Is there a way within the GROMACS suite of programs to evaluate the 
> solvent-accessible area (and volume, and hence the particle density) of 
> a large (3-5 nm) silica particle, which I am currently simulating in 
> aequous solution using OPLS/AA parameters and TIP4P water ? Being able 
> to extract the total charge on such a particle would also be useful. The 
> closest tool I can find is g_density, but I don't think that does quite 
> what I am looking for.
g_sas will compute solvent accessible surface area.

what do you mean with total charge? you should have that information in
your topology, and the most likely answer is 0.


> 
-- 
David.
________________________________________________________________________
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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