AMBER Archive (2004)

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

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Dec 15 2004 - 18:47:05 CST


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_at_rosswalker.co.uk | > | http://www.rosswalker.co.uk/ | PGP Key available on request | > > > > -----Original Message----- > > From: owner-amber_at_scripps.edu > > [mailto:owner-amber_at_scripps.edu] On Behalf Of Ilyas Yildirim > > Sent: 13 December 2004 20:35 > > To: amber_at_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/ - > > --------------------------------------------------------------- > > > > > > -------------------------------------------------------------- > > --------- > > The AMBER Mail Reflector > > To post, send mail to amber_at_scripps.edu > > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu > > > > ----------------------------------------------------------------------- > The AMBER Mail Reflector > To post, send mail to amber_at_scripps.edu > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu > >

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