[gmx-users] Re: Potential energy methanol in a box

[Fabian Casteblanco]

Thanks again for your response.  I appreciate all your help.

On Sat, Apr 23, 2011 at 6:11 PM, Fabian Casteblanco
<fabian.casteblanco at gmail.com> 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.
>
> 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
>



-- 
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.casteblanco at gmail.com