On 9/2/15 9:47 PM, Ebert Maximilian wrote:
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?
Remember to correct for finite size effects in the diffusion constant
(dx.doi.org/10.1021/jp0477147)
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.
More simply, divide <Uliq> by the number of molecules and just simulate one
molecule in the gas phase (infinite cutoffs, no PBC) for <Ugas>.
-Justin
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
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