Fabian Casteblanco wrote:
Hello,
I'm trying to fill a box with methanol using CHARMM FF Parameters. I
also need to do this for ethanol and 1-propanol.
For ethanol, each individual molecule had approximately -19 kJ/mol of
potential energy, then I placed 1000 in a box, performed nvt, npt,
etc. End Result: A negative potential energy (it means that its
stable?) and a density of 0.785 g/cm3 compared to actual 0.789 g/cm3
at 1 atm, 298 K. This result seemed ok.
Negative potential implies net attraction. Positive potential implies net
repulsion. Systems in the condensed phase typically have negative potential
energies, but you should not necessarily equate negative energy with stability.
Unstable systems can have negative potential, too. But if your trajectory
itself is stable, then likely so too is the system you're looking at.
For methanol and 1-propanol, each individual molecule had a larger
24 - 64 kJ/mol respectively, due to Coulomb 1,4 pair interactions (for
example, for methanol between the HA 0.09 and the H 0.43 gives a large
64 kJ/mol). Again placed 1000 each in 2 separate boxes, performed
nvt,npt,etc on each one. End Result: A still positive potential
energy for each box (shouldn't this be negative after running npt? on
both) and a density that was 0.789 g/cm3 (for 1-propanol)compared to
actual 0.803 g/cm3 1-propanol at 1 atm, 298 K. Methanol density a bit
closer 0.787 compared to 0.791 g/cm3.
Negative potential does not simply arise from NPT simulation. The potential is
determined by the topology and functional form used. Something about these
systems is causing a net repulsion, and it may very well be the intramolecular
interactions. That seems likely, since the densities you're getting are
slightly low, indicating that the molecules are insufficiently condensed.
My questions are:
-There should definetly be a positive potential energy after running
npt, correct? Otherwise it wouldn't be stable? I understand that the
No. See above. Ensemble does not dictate whether or not the potential is
positive or negative. The topology does.
1,4 coulomb interactions should cancel out with nearby molecules.
No. 1-4 interactions are intramolecular. They are not dependent upon the
presence or absence of nearby molecules. They are dependent upon the
configurations of the individual molecules themselves.
*For CHARMM, they state that unless otherwise 1,4 parameters exist
already, they use a full scale 1.0 of the regular LJ, coulomb
potential.
Correct.
-As for the density, I know it's somewhat close but I'm trying to be
as accurate as possible. I read somewhere that the average cut-off
(rlist) is usually 1.4 for CHARMM and I had mine set to 1. I'm
guessing that having a larger cutoff would contribute more molecules
to the LJ, coulomb which might rise the density a bit to the correct
value?
The value of the cutoff should be no less than 1.2-1.4 nm, according to the
CHARMM developers (http://dx.doi.org/10.1002/jcc.21287). It's hard to predict
the effects of such changes, since they will affect neighbor searching, balance
of PME terms, and others. You should certainly be using settings recommended
(and used) by the force field developers, unless you have a substantive reason
not to (i.e., someone has developed better settings).
-Justin
I'm still new to Gromacs so I appreciate all of anybodys help. Thanks a bunch.
--
Best regards,
Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E: fabian.castebla...@gmail.com
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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