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
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Received on Sun Oct 23 2005 - 17:53:00 PDT
