Mark Abraham wrote:
JMandumpal wrote:
Dear list,
I would like to simulate aqueous acetone system using UA OPLS
potentials. I chose the following atoms types, given below (TABLE ONE),
for acetone, with united atom for Methyl groups.
TABLE ONE
----------------------------------------------------------------------------------
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 opls_069 1 ACET CAA 1 0.000 15.0350
2 opls_280 1 ACET C_2 1 0.470 12.0110
3 opls_069 1 ACET CAD 1 0.000 15.0350
4 opls_281 1 ACET O_2 1 -0.470 15.9994
-----------------------------------------------------------------------------------
But on the other hand, when I checked the literature, JPC
94, 1990, p.1683, I found out, the parameters are given in the
following manner, TABLE TWO :
TABLE TWO
************************************************************************************
atom types charge sigma epsilon
CH3 0.062 3.910 0.160
C 0.300 3.750 0.105
O -0.424 2.960 0.210
**********************************************************************************
For keeping total charge in the system to zero, I used the opls_069
for methyl group (zero charge), in my input file, compared to what has
been published. I would like to know whether the parameters (charge) I
chose is right, else which atom type I must use for methyl group.
Different models will have different charges. What is correct to use
depends on how those models were parameterized to interact with which
other force fields, and for what purpose they were intended. Finding
this out and making these decisions is your job, not ours.
Apart from that: just test it. Simulate bulk acetone and compare the
properties to experimental data (densite DHvap etc.)
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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