[gmx-users] acetone parameter

[David van der Spoel]

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