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A possibly useful reference for vdw parameters for unit carbon atoms in
hydrocarbons is:<br><br>
<font face="Times, Times">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. <i>J. Phys. Chem.
</font><font face="MS Serif, Geneva"> B </i>103:6323-6327<br><br>
</font>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.<br><br>
Eric <br><br>
At 07:20 PM 1/5/2004 +0100, you wrote:<br>
<blockquote type=cite class=cite cite>On Mon, 5 Jan 2004, Pedro Alexandre
Lapido Loureiro wrote:<br><br>
>Hi!<br>
><br>
>I am doing a parametrization of small alkane with halogen
atoms.<br>
>When the density is good, the DHvap is not (6 kcal/mol - experimental
and 11 <br>
>kcal/mol - my simulation) and vice versa.<br>
>For the calculation, I am using: DHvap = RT - Einter(liquid
state).<br>
>To what extent should I expect to reproduce the experimental DHvap
value? <br>
Better than 6, within 2 kJ/mole, but not for all possible halogenated
<br>
compounds. Can you be more specific? Is this within the OPLS (all-atom)
<br>
force field?<br><br>
Gromacs does have specific options for parameterizing.<br><br>
>Regards,<br>
><br>
>Pedro.<br>
>--<br>
>Pedro Alexandre Lapido Loureiro<br>
>Laboratório de Física Biológica<br>
>Instituto de Biofísica<br>
>UFRJ<br>
>Brasil <br>
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><br><br>
-- <br>
David.<br>
________________________________________________________________________<br>
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics
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---------------------------------<br>
Eric Jakobsson, Ph.D.<br>
Professor, Department of Molecular and Integrative Physiology, and of
Biochemistry<br>
Senior Research Scientist, National Center for Supercomputing
Applications<br>
Professor, Beckman Institute for Advanced Science and Technology<br>
4021 Beckman Institute, mc251<br>
University of Illinois, Urbana, IL 61801<br>
ph. 217-244-2896 fax
217-244-2909<br>
(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.)<br><br>
<br>
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