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

David spoel at xray.bmc.uu.se
Wed Aug 10 14:37:48 CEST 2005

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 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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