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

Steven Kirk Steven.Kirk at htu.se
Tue Aug 9 19:59:37 CEST 2005


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.

In addition, I am looking for quantities which are both obtainable from 
GROMACS simulations (using the standard suite of GROMACS analysis tools 
or other freely available software) and from the range of existing 
experimental techniques used on to examine such systems. Total charge on 
the particle and total dipole moment would also be useful. I am aware 
that in experimental work such techniques as small-angle neutron 
scattering can be used to look at the structure of such particles, but I 
would like to establish a list of properties that are both 
experimentally and computationally available.

I have searched through the list archive already and found some 
interesting discussions of pH, but it seems that detailed considerations 
of pH is not easy in GROMACS. I have seen a few papers in the literature 
  that use a Monte-Carlo approach to playing with protonation states on 
solvated proteins to mimic a constant pH, but it seems that there is no 
consensus yet on the best way to computationally evaluate such quantities.

I would appreciate any advice and recommendations for software (advice 
from other researchers investigating such colloidal systems would be 
especially welcome).

Many thanks in advance,
Steve Kirk

Dr. Steven R. Kirk          <Steven.Kirk at htu.se, S.R.Kirk at physics.org>
Dept. of Computer Science, TMD               http://taconet.webhop.org
Univ. of Trollhattan/Uddevalla   Ph: +46 520 475318 Fax:+46 520 475399
P.O. Box 957 Trollhattan 461 29 SWEDEN

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