[gmx-users] Enthalpy of vaporization
jake at ncsa.uiuc.edu
Mon Jan 5 22:26:02 CET 2004
A possibly useful reference for vdw parameters for unit carbon atoms in
Chiu, S. W., Clark, M. M., Jakobsson, E., Subramaniam, S., and H. L. Scott.
1999b. Optimizations of hydrocarbon chain interaction parameters:
Application to the simulation of fluid phase lipid bilayers. J. Phys.
Chem. B 103:6323-6327
The main point is that in order to get the parameters right, you need to
simulate the density at constant pressure for plymers with the same
building blocks, but different numbers of them. In that case at least, the
same parameters that worked for the density also made the heat of
vaporization about right.
At 07:20 PM 1/5/2004 +0100, you wrote:
>On Mon, 5 Jan 2004, Pedro Alexandre Lapido Loureiro wrote:
> >I am doing a parametrization of small alkane with halogen atoms.
> >When the density is good, the DHvap is not (6 kcal/mol - experimental
> and 11
> >kcal/mol - my simulation) and vice versa.
> >For the calculation, I am using: DHvap = RT - Einter(liquid state).
> >To what extent should I expect to reproduce the experimental DHvap value?
>Better than 6, within 2 kJ/mole, but not for all possible halogenated
>compounds. Can you be more specific? Is this within the OPLS (all-atom)
>Gromacs does have specific options for parameterizing.
> >Pedro Alexandre Lapido Loureiro
> >Laboratório de Física Biológica
> >Instituto de Biofísica
> >gmx-users mailing list
> >gmx-users at gromacs.org
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>David van der Spoel, PhD, Assist. 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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Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896 fax 217-244-2909
(Currently on leave to the National Institutes of Health in Bethesda,
Maryland, to be Director of the NIGMS Center for Bioinformatics and
Computational Biology and Chair of the NIH Biomedical Information Science
and Technology Initiative Consortium, but maintaining my research lab at
Illinois by periodic commuting. My usual schedule is four days a week at
NIH and three days a week at Illinois.)
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