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 <vvcha...@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.eb...@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 <vvcha...@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.eb...@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.lu...@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.lu...@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.eb...@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 >>>>>>> -- >>>>>>> Gromacs Users mailing list >>>>>>> >>>>>>> * Please search the archive at >>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>>>> posting! >>>>>>> >>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>>> >>>>>>> * For (un)subscribe requests visit >>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>>>>> send a mail to gmx-users-requ...@gromacs.org. >>>>>> >>>>>> >>>>>> >>>>> -- >>>>> Gromacs Users mailing list >>>>> >>>>> * Please search the archive at >>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>>> posting! >>>>> >>>>> * Can't post? 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