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

Thu Sep 3 04:27:18 CEST 2015

Hi justin,

thank you for the answer. From your experience to calculate the shear viscosity with gmx tcaf for the correction term your mentioned (2.837297kBT/(6πηL)) would a trajectory with coordinates and velocities every 1 ps enough?

Thanks

On Sep 2, 2015, at 9:55 PM, Justin Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:

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<http://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 <vvchaban at gmail.com<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu<mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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