[gmx-users] OPLS/AA parameters for 2-propanol

Ebert Maximilian m.ebert at umontreal.ca
Thu Sep 3 03:52:58 CEST 2015 

Thanks for the answer again. So I saw that for self-diffusion and viscosity I can just use gmx tcaf and gmx msd. As an experimental setup, would a squared box with 500 molecules of 2-propanol in NPT equilibration for a 10ns be a good system to use tcaf and msd?

For the heat of vaporization I saw that I could calculate DHvap = <Ugas> - <Uliq> + RT 

<Uliq>  is just Epot of the same MD I described above but for <Ugas> I need a new calculation. If I understood it correctly I would need a box with the same number of molecules as in the previous calculation but separate them with a lot of space (50nm was suggested). In addition, turn off PBC, PME, L-J and coulomb cut-offs. Get Epot from this calculation and use the formular. 

Would these approaches be correct?

Thank you very much. 

Max

> On Sep 2, 2015, at 5:02 PM, Vitaly V. Chaban <vvchaban at gmail.com> wrote:
> 
> It is difficult to get a very wrong density, especially for relatively
> rigid compounds. In the meantime, deviations of density within 2% of
> the experimental value should be admitted acceptable.
> 
> A better criterion is to compare self-diffusion or viscosity to the
> experiment. Another famous property for parametrization is heat of
> vaporization.
> 
> 
> 
> 
> 
> 
> On Wed, Sep 2, 2015 at 3:22 PM, Ebert Maximilian <m.ebert at umontreal.ca> wrote:
>> Thanks for the reply. I think I found relatively good atom types for iso propanol and derived the partial charges using antechamber and red server. I next check the density of pure iso propanol and used the closest definition to the real value. Iso propanol is used as co-solvent with water with a water:iso propanol ration of 90:10. I will just use my derived parameters then.
>> 
>> Thanks for your replies.
>> 
>> Max
>> 
>>> On Sep 2, 2015, at 2:08 PM, Vitaly V. Chaban <vvchaban at gmail.com> wrote:
>>> 
>>> Normally, this sort of things is done via mechanical combining of the
>>> known groups --  CH3, -CH, OH -- from the force field.
>>> 
>>> If your goal is to increase accuracy for pure 2-propanol per se, then
>>> play with the distribution of electronic density between OH and CH.
>>> 
>>> If 2-propanol is to be used as a solvent for somwthing else, this does
>>> ultimately not pay off.
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>>> On Wed, Sep 2, 2015 at 11:42 AM, Ebert Maximilian <m.ebert at umontreal.ca> wrote:
>>>> I saw the papers you mentioned but one is a not clear how they parameterized, one is missing the supporting material and the last is not showing the parameters they used. I will check with the initial paper of Jorgensen again but if I recall it correctly he mentioned some problems with iso-propanol.
>>>> 
>>>> strange that such a common organic solvent is not easily accessible for OPLS.
>>>> 
>>>> thanks for your help johnny!
>>>> 
>>>> Max
>>>> 
>>>>> On Sep 1, 2015, at 11:41 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
>>>>> 
>>>>> that was by google. I haven't parametrized forcefields.
>>>>> did they just put the pieces in
>>>>> http://pubs.acs.org/doi/abs/10.1021/ja9621760 together and say it can work
>>>>> for 2-propanol?
>>>>> 
>>>>> 
>>>>>> On Tue, Sep 1, 2015 at 11:34 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
>>>>>> 
>>>>>> Not sure if those are for 2-propanol as a liquid or interaction between
>>>>>> 2-propanol and protein.
>>>>>> from googling "2 propanol opls/aa"
>>>>>> 
>>>>>> 1. Development and Testing of the OPLS All-Atom Force Field on
>>>>>> Conformational Energetics and Properties of Organic Liquids
>>>>>>    The parameters are in the supporting info.
>>>>>>    Seems not exactly 2-propanol. But it has parameter for organic
>>>>>> liquids.
>>>>>>    "OPLS-AA Non-Bonded Parameters for Hydrocarbons and Alcohols"
>>>>>>    http://pubs.acs.org/doi/abs/10.1021/ja9621760
>>>>>> 
>>>>>> 2. A statistical model of hydrogen bond networks in liquid alcohols
>>>>>> 
>>>>>> http://publications.lib.chalmers.se/records/fulltext/local_157930.pdf
>>>>>> 
>>>>>> 3. Parameterization of OPLS–AA Force Field for the Conformational Analysis
>>>>>> of Macrocyclic Polyketides
>>>>>>    https://labs.chem.ucsb.edu/bruice/thomas/tcb_pdf/522.pdf
>>>>>> 
>>>>>> On Tue, Sep 1, 2015 at 9:41 PM, Ebert Maximilian <m.ebert at umontreal.ca>
>>>>>> wrote:
>>>>>> 
>>>>>>> Dear list,
>>>>>>> 
>>>>>>> I wanted to know if anybody has parameters for 2-propanol in the OPLS/AA
>>>>>>> format. Before deriving my own I thought it would be best to ask first. I
>>>>>>> saw some posts that people used 2-propanol in OPLS but couldn’t find any
>>>>>>> reference in google scholar.
>>>>>>> 
>>>>>>> Thank you very much,
>>>>>>> 
>>>>>>> Max
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