On 9/2/15 10:24 PM, Ebert Maximilian wrote:
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?
Probably.
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
mailto:ja
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 t
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 sa
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
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
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 s
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-propa
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 wrote:
> Not sure if those are for 2-propanol as a liquid or interaction
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 i
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
--
Gro
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