RE: AMBER: Workshop 2004, Tutorial #6, QMMM MD Simulation

From: Ilyas Yildirim <yildirim.pas.rochester.edu>
Date: Wed, 15 Dec 2004 19:47:05 -0500 (EST)

Hi Ross,

After patching the bugfix, I did not get the error messages I was getting
before. But I got really strange results which I wanted to ask you about.

The starting .parm and .inpcrd files I am using are taken from your
tutorial. The classical MD simulation results I am getting are
same you got. But the QMMM minimisation results I am getting are
different than your results (as a result the QMMM MD sim results are
different too). Here are the input files I am using for the
QMMM min and MD simulations.

----------- min_qmmm.in -------------
Initial min of our structure QMMM
 &cntrl
  imin=1, maxcyc=500, ncyc=200,
  cut=20, ntb=0, fcap=1.5,
  ifqt=1, nqt=12, idc=0
 /
 1 2 3 4 5 6 7 8 9 10 11 12
END
END
-------------------------------------
------------ md_qmmm.in -------------
300K constant temp QMMMMD
 &cntrl
  imin=0, ntb=0,
  cut=20, fcap=1.5,
  tempi=300.0, temp0=300.0,
  ntt=3, gamma_ln=1.0,
  nstlim=1000, dt=0.001,
  ntpr=1, ntwx=1,
  ifqt=1, nqt=12, idc=0
 /
 1 2 3 4 5 6 7 8 9 10 11 12
END
END
------------------------------------
------------ divcon.in -------------
CARTESIAN PM3 CHARGE=0 &
STANDARD DIRECT
END_COORD
------------------------------------

The original results are the following (published in the tutorial)
-----------------------------------------------------------------------------
                    FINAL RESULTS



   NSTEP ENERGY RMS GMAX NAME NUMBER
    500 -4.6525E+03 6.0593E-01 7.7037E+00 C 5

 BOND = 343.7006 ANGLE = 0.0000 DIHED =
0.0000
 VDWAALS = 982.1865 EEL = -5917.1502 HBOND =
0.0000
 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
0.0000
 ESCF = -61.1920
------------------------------------------------------------------------------

The results I got are the following:
----------------------------------------------------------------------------
                    FINAL RESULTS



   NSTEP ENERGY RMS GMAX NAME NUMBER
    500 -4.6486E+03 7.8047E-01 1.0472E+01 CH3 2

 BOND = 346.0135 ANGLE = 0.0000 DIHED =
0.0000
 VDWAALS = 980.6513 EEL = -5914.4172 HBOND =
0.0000
 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
0.0000
 ESCF = -60.8476
----------------------------------------------------------------------------

Are these differences (Energy, RMS) reasonable?

Another thing is with the QMMM MD simulation. Here is the result I got:
----------------------------------------------------------------------------
 NSTEP = 999 TIME(PS) = 0.999 TEMP(K) = 268.73 PRESS =
0.0
 Etot = -2847.2054 EKtot = 990.8776 EPtot =
-3838.0830
 BOND = 688.1413 ANGLE = 0.0000 DIHED =
0.0000
 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
922.8630
 EELEC = -5399.6868 EHBOND = 0.0000 RESTRAINT =
0.0000
 ESCF = -49.4004

-----------------------------------------------------------------------------

Here, TEMP(K) = 268.73. Is this normal? (In the original md_qmmm.out file
in the tutorial, the temp is approx the same) In the md_qmmm.in file, the
final temp given is 300. So, I was wondering if it is reasonable to get
this final temp.

Thanks in advance.

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -                              -
  - University of Rochester      -                              -
  - Hutchison Hall, Office B10   -                              -
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) -
  - http://www.pas.rochester.edu/~yildirim/                     -
  ---------------------------------------------------------------
On Tue, 14 Dec 2004, Ross Walker wrote:
> Dear Ilyas
>
> Have you applied the two QMMM bug fixes to your amber 8 installation and
> re-compiled sander.QMMM? See
>
> http://amber.scripps.edu/bugfixes/8.0/bugfix.13
>
> And
>
> http://amber.scripps.edu/bugfixes/8.0/bugfix.26
>
> The latter one should not effect the tutorial results as it only deals with
> problems with link atoms.
>
> Check if the tests pass once you have applied the fixes. Make
> test.sander.QMMM.
>
> You should be able, if you use exactly the same files as on the tutorial,
> reproduce the tutorial results to within round off error. Can you post me
> your output file.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
>
> > -----Original Message-----
> > From: owner-amber.scripps.edu
> > [mailto:owner-amber.scripps.edu] On Behalf Of Ilyas Yildirim
> > Sent: 13 December 2004 20:35
> > To: amber.scripps.edu
> > Subject: AMBER: Workshop 2004, Tutorial #6, QMMM MD Simulation
> >
> > Hi all,
> >
> > While I was following the Workshop 2004, tut. #6, I
> > encountered a problem
> > with the QMMM MD simulation part. The minimisation procedure of QMMM
> > method gives the following error:
> >
> > ...
> >      .... RESTARTED DUE TO LINMIN FAILURE ...
> >
> >      ***** REPEATED LINMIN FAILURE *****
> > ...
> >
> > I even have copied/pasted the files for QMMM min. part given in the
> > tutorial, and still got the same error. The input files are
> > here (given in the
> > http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_
> > Six/index.htm
> > webpage)
> >
> > divcon.in
> > -------------------
> > CARTESIAN PM3 CHARGE=0 &
> > STANDARD DIRECT
> > END_COORD
> > -------------------
> >
> > min_qmmm.in
> > -------------------
> > Initial min of our structure QMMM
> >  &cntrl
> >   imin=1, maxcyc=500, ncyc=200,
> >   cut=20, ntb=0, fcap=1.5,
> >   ifqt=1, nqt=12, idc=0
> >  /
> >  1 2 3 4 5 6 7 8 9 10 11 12
> > END
> > END
> > -------------------
> >
> > md_qmmm.in
> > -------------------
> > 300K constant temp QMMMMD
> >  &cntrl
> >   imin=0, ntb=0,
> >   cut=20, fcap=1.5,
> >   tempi=300.0, temp0=300.0,
> >   ntt=3, gamma_ln=1.0,
> >   nstlim=1000, dt=0.001,
> >   ntpr=1, ntwx=1,
> >   ifqt=1, nqt=12, idc=0
> >  /
> >  1 2 3 4 5 6 7 8 9 10 11 12
> > END
> > END
> > ------------------
> >
> > The NMA.prmtop and NMA.inpcrd files are exactly the same
> > files given in
> > the above given website. Anyone having any idea why I am getting these
> > errors? I have installed AMBER 8 to a DELL 5100, P4 laptop,
> > with a SUSE
> > Linux 9.1 Personal Edition. Thanks in advance...
> >
> > Ciao,
> >
> > --
> >   Ilyas Yildirim
> >   ---------------------------------------------------------------
> >   - Department of Chemisty       -                              -
> >   - University of Rochester      -                              -
> >   - Hutchison Hall, Office B10   -                              -
> >   - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) -
> >   - http://www.pas.rochester.edu/~yildirim/                     -
> >   ---------------------------------------------------------------
> >
> >
> > --------------------------------------------------------------
> > ---------
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> >
>
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Received on Thu Dec 16 2004 - 00:53:00 PST