[gmx-users] acetone parameter
David van der Spoel
spoel at xray.bmc.uu.se
Fri Apr 18 08:16:15 CEST 2008
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.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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