Indeed there is a nonpolar hydrogen close to the
hydroxide. I have to delete the bond which is
recognized by xleap. However I'm still surprised that
there are no vdw changes at all since the hydroxide
disappears in the final molecule.
Here is the result of vacuum simulation.
A V E R A G E S O V E R 50000 S T E P S
NSTEP = 100000 TIME(PS) = 200.000 TEMP(K) =
299.89 PRESS = 0.0
Etot = -88.4882 EKtot = 32.4791
EPtot = -120.9673
BOND = 8.2543 ANGLE = 24.0244
DIHED = 14.4280
1-4 NB = 18.1261 1-4 EEL = -283.9862
VDWAALS = -1.4587
EELEC = 99.6448 EHBOND = 0.0000
RESTRAINT = 0.0000
DV/DL = 168.3202
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 100000 TIME(PS) = 200.000 TEMP(K) =
28.64 PRESS = 0.0
Etot = 0.1691 EKtot = 3.1015
EPtot = 3.1343
BOND = 2.2408 ANGLE = 2.9717
DIHED = 2.0345
1-4 NB = 1.7082 1-4 EEL = 3.8453
VDWAALS = 1.9314
EELEC = 3.3446 EHBOND = 0.0000
RESTRAINT = 0.0000
DV/DL = 3.8538
------------------------------------------------------------------------------
DV/DL, AVERAGES OVER 50000 STEPS
NSTEP = 100000 TIME(PS) = 200.000 TEMP(K) =
0.00 PRESS = 0.0
Etot = 0.0000 EKtot = 0.0000
EPtot = 168.3202
BOND = 0.0000 ANGLE = 0.0000
DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 154.8224
VDWAALS = 0.0000
EELEC = 13.4979 EHBOND = 0.0000
RESTRAINT = 0.0000
------------------------------------------------------------------------------
--- "David A. Case" <case.scripps.edu> wrote:
> On Tue, Feb 22, 2005, Eric Hu wrote:
>
> > Ok, I perturbed one molecule to another which
> lacks by
> > a hydroxide only. I am thinking maybe I should
> > calculate the energy difference by perturbing both
> > molecules to nothing to prevent such big dV/dL
> values.
>
> That should not be necessary.
>
> > R M S F L U C T U A T I O N S
> > DV/DL = 54.2857
> >
>
------------------------------------------------------------------------------
> > DV/DL, AVERAGES OVER 500000 STEPS
> >
> >
> > NSTEP = 1000000 TIME(PS) = 1020.000
> TEMP(K) =
> > 0.00 PRESS = 0.0
> > Etot = 0.0000 EKtot = 0.0000
> EPtot = 1465.4880
> > BOND = 0.0000 ANGLE = 0.0000
> DIHED = 0.0000
> > 1-4 NB = 0.0000 1-4 EEL = 883.5451
> VDWAALS = 0.0000
> > EELEC = 581.9429 EHBOND = 0.0000
> RESTRAINT = 0.0000
> > Ewald error estimate: -0.1636E-04
> >
>
> It's not at all clear why the DV/DL values are so
> high; I would try a vacuum
> simulation at the same lambda to see if that helps.
> Do you have close
> intramolecular interactions with the OH group that
> you are changing?
>
> You should certainly try to decouple the
> electrostatic and atom-type changes
> if you are not already doing so. (The output
> snippet from above shows only
> electrostatic changes, so maybe that is already a
> problem.)
>
> ...dac
>
>
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Received on Wed Feb 23 2005 - 23:53:00 PST
