AMBER Archive (2005)

Subject: Re: AMBER: a bimolecular reaction

From: Eric Hu (eric.y.hu_at_gmail.com)
Date: Tue Apr 12 2005 - 18:50:58 CDT

Thank you, Yong. The force parameters (bond, angle and etc) change
coupled with atom type changes. Since the two molecules eventually
become one, the CX---OX distance decreases to a normal C-OS distance.
The bond energy jumps to very high at the beginning of the vdw
perturbation and remains throughout the simulation, which makes me
think that TI is not very suitable for bond making process. Here is a
summary of the input and out files.

Eric

  &cntrl
  ntr=0,
  nstlim =100000, nscm=2000, ntave=5000,
  ntx=5, irest=1, ntb=0, ntpr=100,
  ntp=0, taup=2.0,
  dt=0.001, nrespa=2,
  ntt=0, temp0 = 300., tautp=2.0,
  ntc=2, ntf=2, tol=0.000001,
  ntwr = 100, ntwx=1000,
  icfe=1, klambda=6, clambda=0.05,
 cut=999,
/

|===============================================================================

      A V E R A G E S O V E R 50000 S T E P S

  NSTEP = 100000 TIME(PS) = 120.000 TEMP(K) = 319.75 PRESS = 0.0
  Etot = 1891.4011 EKtot = 35.9003 EPtot = 1855.5008
  BOND = 1746.5250 ANGLE = 40.3842 DIHED = 58.1878
  1-4 NB = 15.0713 1-4 EEL = 0.0000 VDWAALS = -4.6675
  EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = 0.0000
  DV/DL = 19685.1423
 ------------------------------------------------------------------------------

      R M S F L U C T U A T I O N S

  NSTEP = 100000 TIME(PS) = 120.000 TEMP(K) = 30.42 PRESS = 0.0
  Etot = 0.0610 EKtot = 3.4150 EPtot = 3.4541
  BOND = 2.4338 ANGLE = 3.3799 DIHED = 2.2930
 1-4 NB = 1.5695 1-4 EEL = 0.0000 VDWAALS = 1.0556
 EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = 0.0000
 DV/DL = 489.7961
|E(PBS) = 0.0465
 ------------------------------------------------------------------------------

      DV/DL, AVERAGES OVER 50000 STEPS

 NSTEP = 100000 TIME(PS) = 120.000 TEMP(K) = 0.00 PRESS = 0.0
 Etot = 0.0000 EKtot = 0.0000 EPtot = 19685.1423
 BOND = 19464.7683 ANGLE = 19.2493 DIHED = 206.2587
 1-4 NB = -9.6047 1-4 EEL = 0.0000 VDWAALS = 4.4709
 EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = 0.0000
 ------------------------------------------------------------------------------

On 4/12/05, duan_list_at_albert.genomecenter.ucdavis.edu
<duan_list_at_albert.genomecenter.ucdavis.edu> wrote:
>
> This was probably caused by one (or more) atoms that seem to have
> charges, yet without van der Waals, at the unperturbed (initial) state.
> Note, "HO" also has a zero van der Waals radius and is likely involved in
> this "fussion" process. Other possibilities include the dummy atoms, if
> you have any. If you only want to let the atom disappear, the atoms should
> also have bonds, etc, at the unperturbed state, unless, somehow the bond
> (and angle) parameters became zero.
>
> Good luck!
>
> yong
> On Tue, 12 Apr 2005, David A. Case wrote:
>
> > On Wed, Apr 06, 2005, Eric Hu wrote:
> >
> > > Hi, I am experimenting a TI perturbation with Amber 8.0 on an
> > > enzyme-catalyzed bimolecular reaction (an alcohol reacts with a
> > > carboxylic acid to form an ester).
> > >
> > > NSTEP ENERGY RMS GMAX NAME NUMBER
> > > 200 -1.1864E+07 2.6376E+11 2.1022E+12 H15 15
> > >
> > > BOND = 6.6603 ANGLE = 78.2334 DIHED = 38.3939
> > > VDWAALS = -2.9575 EEL = 54.6011 HBOND = 0.0000
> > > 1-4 VDW = 12.2257 1-4 EEL = ************* RESTRAINT = 0.0000
> >
> > Take a look visually at the structure after 150 steps or so, and see if you
> > can figure out which atoms are getting close to each other (leading to a very
> > large, negative 1-4 EEL term). That might provide some clue, although I don't
> > know why the 1-4 vdw is not increasing...
> >
> > ...dac
> >
>
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