[gmx-users] Potential energy methanol in a box

Fabian Casteblanco fabian.casteblanco at gmail.com
Sun Apr 24 00:11:42 CEST 2011

```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.

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.

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
1,4 coulomb interactions should cancel out with nearby molecules.
*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.

-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?

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.casteblanco at gmail.com
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```