AMBER Archive (2009)

Subject: [AMBER] NAB md function prints strange output

From: Jochen Heil (jheil_at_keychem.de)
Date: Mon Feb 09 2009 - 05:30:21 CST

Hi,
i am trying to mimick the structure preparation of the score24 protocol
of DOCK6 with NAB. The CG minimization seems to work as expected whereas
the MD routine behaves strange. For some reason, i get "nan" for the
total energy as well as the nonpolar part. Since i switched off GBSA, i
would expect zero, but "nan" seems to point to a wrong setup or logical
error, especially when printed in the total energy column. We have
looked at the MD trajectory and found nothing suspicious, e.g. no
clashes. Is this just NABs behaviour or is there an obvious problem with
my settings?

Input options are taken from the DOCK implementation:
For CG: diel=C, gbsa=0, nsnb=99999, cut=18.0, gb=5
For MD:diel=C, dt=0.001, gamma_ln=2, rattle=0, cut=18.0, gb=5,
tempi=300.0, temp0=300.0, ntwx=10

Output from CG is:

Reading parm file
(complex.prmtop)

title:

                                                                                                                                                     

        mm_options:
diel=C

        mm_options:
gbsa=0

        mm_options:
nsnb=99999

        mm_options:
cut=18.0

        mm_options:
gb=5

constrained all 5606
atoms

freezing 5556 atoms using expression
1:235:CA|1:235:CB|1:235:HB2|1:235:HB3|1:235:CG|1:235:CD2|1:235:HD2|1:235:C|1:235:O|1:236:N|1:237:HB3|1:242:HG2|1:242:HE3|1:242:HZ3|1:243:HA|1:243:HG|1:246:CG|1:246:CD1|1:246:CE1|1:246:HE1|1:246:CZ|1:246:OH|1:246:HH|1:246:CE2|1:246:HE2|1:246:CD2|1:246:HD2|1:351:C1|1:351:O|1:351:N2|1:351:C3|1:351:C4|1:351:C4A|1:351:C5|1:351:C6|1:351:C7|1:351:C8|1:351:C8A|1:351:C9|1:351:H|1:351:H1|1:351:H2|1:351:H3|1:351:H4|1:351:H5|1:351:H6|1:351:H7|1:351:H8|1:351:H9|1:351:H10
for moving
atoms

      iter Total bad vdW elect nonpolar
genBorn frms
ff: 0 6.28 31.18 -20.13 -95.67 0.00 90.89
8.07e-01
ff: 10 -1.58 30.53 -26.38 -96.69 0.00 90.96
3.93e-01
ff: 20 -6.36 29.95 -29.17 -98.03 0.00 90.90
2.45e-01
ff: 30 -8.55 29.74 -30.31 -98.92 0.00 90.94
2.34e-01
ff: 40 -10.00 29.93 -31.50 -99.28 0.00 90.86
1.65e-01
ff: 50 -11.36 29.70 -31.90 -99.49 0.00 90.33
1.36e-01
ff: 60 -11.98 29.87 -32.01 -99.96 0.00 90.12
1.25e-01
ff: 70 -12.62 29.89 -32.09 -100.31 0.00 89.89
1.04e-01
ff: 80 -13.13 30.09 -32.09 -100.32 0.00 89.19
7.53e-02
ff: 90 -13.47 30.20 -31.80 -100.67 0.00 88.79
8.65e-02
ff: 100 -13.89 30.13 -31.38 -100.99 0.00 88.35
1.10e-01

The Conjugate gradient minimization returns maximum number of iterations
exceeded.

A sample from the MD output:

Starting MD simulation!

        mm_options: diel=C
        mm_options: dt=0.001
        mm_options: gamma_ln=2
        mm_options: rattle=0
        mm_options: cut=18.0
        mm_options: gb=5
        mm_options: tempi=300.0
        mm_options: temp0=300.0
        mm_options: ntwx=10
      iter Total bad vdW elect nonpolar
genBorn frms
ff: 0 nan 30.13 -31.38 -100.99 nan 88.35
1.10e-01
md: 1 0.001 45.88 nan nan
307.85
ff: 10 nan 51.78 -30.57 -101.70 nan 88.74
1.32e+00
md: 10 0.010 27.96 nan nan
187.60
ff: 20 nan 54.86 -29.80 -101.20 nan 87.84
1.43e+00
md: 20 0.020 23.99 nan nan
160.98
ff: 30 nan 57.01 -28.80 -102.55 nan 87.74
1.52e+00
md: 30 0.030 22.44 nan nan
150.59
ff: 40 nan 51.73 -28.45 -99.72 nan 86.37
1.54e+00
md: 40 0.040 27.35 nan nan
183.49
...

The return value of the MD function is zero.

Best regards,
Jochen 

-- 

Dipl.-Ing. Jochen Heil
AG Kast
Eduard-Zintl-Institut für Anorganische und Physikalische Chemie
Technische Universität Darmstadt
Petersenstr. 20, 64287 Darmstadt, Germany

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber