AMBER Archive (2005)

Subject: AMBER: Problem with the QMMM example in AMBER 2004 tutorial

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Sun Oct 23 2005 - 11:31:45 CDT

Dear Amber community,

I have been going through the QMMM example for NMA in
AMBER 2004 tutorial.
Instead of building NMA from scratch, I used the ACE
and NME residues in leap from Cornell et al.(1995) in
AMBER force field 1999 to constitute NMA (i.e.; NMA =
sequence {NME ACE} in leap). I then solvated NMA with
solvatecap and prepared prmtop and crd files for NMA.

I preminimized the solvated NMA with the min_qmmm.in
(maxcyc=500) and divcon.in provided in the tutorial.
However, the minimization process stoped at step=314.
Here is the qmmm output for the minimization:
----------------------------------------------------
NSTEP ENERGY RMS GMAX
 NAME NUMBER
    300 -3.5459E+03 9.2560E+01 1.0814E+03
    H2 612

 BOND = 238.9776 ANGLE = 0.0000
DIHED = 0.0000
 VDWAALS = 408.9435 EEL = -4120.5053
HBOND = 0.0000
 1-4 VDW = 0.0000 1-4 EEL = 0.0000
RESTRAINT = 0.0000
 ESCF = -73.3595

     .... RESTARTED DUE TO LINMIN FAILURE ...

     ***** REPEATED LINMIN FAILURE *****

                    FINAL RESULTS

   NSTEP ENERGY RMS GMAX
    NAME NUMBER
    314 -3.5459E+03 9.7263E+01 1.0969E+03
    H2 612

 BOND = 238.9806 ANGLE = 0.0000
DIHED = 0.0000
 VDWAALS = 408.9436 EEL = -4120.5050
HBOND = 0.0000
 1-4 VDW = 0.0000 1-4 EEL = 0.0000
RESTRAINT = 0.0000
 ESCF = -73.3597
 

-----------------------------------------
 
 
I decided to keep going with the final coordinates of
the minimization job and ran a QMMM-MD job using the
md-qmmm.in (nstlim=1000) input provided in the
tutorial.

However, the temperature of the NMA system went up to
400000 K blowing up the solvated system. All water
molecules boiled off into space.
Here is the QMMM energy output for the final steps of
the MD-QMMM job.
----------------------------------------------------
vlimit exceeded for step 998 ; vmax =
45.1848515305484

 NSTEP = 999 TIME(PS) = 0.999 TEMP(K)
=395387.59 PRESS = 0.0
 Etot = 2898441.6873 EKtot = 1457886.6204
EPtot = 1440555.0670
 BOND = 1440662.7705 ANGLE = 0.0000
DIHED = 0.0000
 1-4 NB = 0.0000 1-4 EEL = 0.0000
VDWAALS = 2.4905
 EELEC = -110.1941 EHBOND = 0.0000
RESTRAINT = 0.0000

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

 vlimit exceeded for step 999 ; vmax =
45.1525855541494

   KE Trans = 39950.1492 KE Rot = 2102.0829
C.O.M. Vel = 3.276724

   Translational and rotational motion removed

   KE Trans = 0.0000 KE Rot = 0.0000
C.O.M. Vel = 0.000000

 NSTEP = 1000 TIME(PS) = 1.000 TEMP(K)
=395966.90 PRESS = 0.0
 Etot = 2900255.4727 EKtot = 1460022.6876
EPtot = 1440232.7851
 BOND = 1440337.7703 ANGLE = 0.0000
DIHED = 0.0000
 1-4 NB = 0.0000 1-4 EEL = 0.0000
VDWAALS = 1.3288
 EELEC = -106.3140 EHBOND = 0.0000
RESTRAINT = 0.0000

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

      A V E R A G E S O V E R 1000 S T E P S

 NSTEP = 1000 TIME(PS) = 1.000 TEMP(K)
=501422.63 PRESS = 0.0
 Etot = 3052035.7321 EKtot = 1848862.6641
EPtot = 1203173.0680
 BOND = 1192589.8404 ANGLE = 0.0000
DIHED = 0.0000
 1-4 NB = 0.0000 1-4 EEL = 0.0000
VDWAALS = 10009.7791
 EELEC = 864.6644 EHBOND = 0.0000
RESTRAINT = 0.0000
----------------------------------------------------

Could some of you please let me know how min_qmmm.in
and md_qmmm.in inputs in the tutorial can be improved
so that the temperature of the system equilibrates
well?

regards,

jenk

    

                
__________________________________
Yahoo! FareChase: Search multiple travel sites in one click.
http://farechase.yahoo.com
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu