On Mon, Feb 29, 2016 at 9:02 PM, Starovoytov, Oleg <ostarovo.central.uh.edu>
wrote:
> Hi Guys,
>
> Just a few questions regarding toluene set up and run.
>
> Trying to set up toluen 216 molecules:
>
> antechamber -i toluene.mol2 -fi mol2 -o toluene.pdb -fo pdb
> antechamber -i toluene.pdb -fi pdb -o toluene.mol2 -fo mol2 -c bcc
> parmchk -i toluene.mol2 -f mol2 -o toluene.frcmod
>
> then in tleap
>
> source leaprc.gaff
> TOL = loadmol2 toluene.mol2
> loadamberparams toluene.frcmod
> BULK = loadpdb TOLUENE.pdb
> setbox BULK centers
> saveAmberParm BULK TOLUENE_216.prmtop TOLUENE_216.inpcrd
> quit
>
> then running min, eql, and production. Running production gives
>
> NSTEP = 177900 TIME(PS) = 357.800 TEMP(K) = 329.83 PRESS =
> -40.7
> Etot = 3895.3213 EKtot = 2619.1565 EPtot =
> 1276.1648
> BOND = 570.2390 ANGLE = 1053.1037 DIHED =
> 688.1559
> 1-4 NB = 961.6047 1-4 EEL = -963.6260 VDWAALS =
> -1601.8145
> EELEC = 568.5021 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 199.0413 VIRIAL = 234.9427 VOLUME =
> 40887.3038
> Density =
> 0.8082
> Ewald error estimate: 0.2108E-04
>
> Questions are
>
> Why is EPtot positive?
>
Because single-point energies are arbitrary and meaningless, *especially*
in standard force fields. For example, take a simple hydrogen molecule at
its equilibrium bond length. The force field would say this energy is 0
kcal/mol (x-xeq == 0). QM, on the other hand, gives a very large negative
number (maybe this is why you expect it to be negative?). In FFs, bonds
and angles can *only* be positive (since the lowest attainable value is
0). Dihedrals can be negative, but clearly in this case are not. I
wouldn't expect the electrostatic interactions to be very large (indeed,
the total electrostatic energy is ~-400 kcal/mol, which is fairly small
compared to the equivalent system of waters where electrostatic
interactions are a lot stronger).
Likewise, the van der Waals eneriges are only ~-700 kcal/mol total, since
dispersion interactions are not terribly strong. Add in the fact that your
system has a *lot* of bonds and angles -- all of which add positive
energies for any distortions from equilibrium geometries -- and you're left
with a situation where the total potential energy is positive. But there's
no reason to suspect this is wrong simply because the energies are positive.
> Why are the Angle, Bond, and DIHED so huge ?
>
They don't look that huge to me... Remember energies are extensive -- the
more bonds and angles you have, the larger those energies will be. Same
with dihedrals.
>
> What is wrong with the set up?
>
From your information, it's impossible to tell if there *is* anything
wrong with your setup. There might be, but we would have no idea based on
the information you gave here.
This is really just the same thing Dave said, though, in a bit of a
different way.
HTH,
Jason
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Received on Mon Feb 29 2016 - 20:30:03 PST
