Hello. I am trying to use nmode to do some vibrational analysis on
some molecules. Since this is the first time I use it I am trying it with
something as simple as CH2=CH2. Now, I created the topology and coords
files using xleap. These are the files
Coordinate file
more eth.crd
eth
6
3.5369136 1.4228577 -0.0000019 4.0237834 0.5493831 -0.0000030
4.0503807 2.2809669 -0.0000033 2.1870839 1.4442981 -0.0000003
1.7014626 2.3173233 -0.0000016 1.6735531 0.5850618 0.0000011
Topology file
more eth.top
%VERSION VERSION_STAMP = V0001.000 DATE = 07/01/03 15:48:48
%FLAG TITLE
%FORMAT(20a4)
eth
%FLAG POINTERS
%FORMAT(10I8)
6 2 4 1 6 0 4 0 0
0
16 1 1 0 0 2 2 1 2
0
0 0 0 0 0 0 0 0 6
0
0
%FLAG ATOM_NAME
%FORMAT(20a4)
C1 H3 H4 C2 H5 H6
%FLAG CHARGE
%FORMAT(5E16.8)
-3.97246140E+00 1.98623070E+00 1.98623070E+00 -3.97246140E+00
1.98623070E+00
1.98623070E+00
%FLAG MASS
%FORMAT(5E16.8)
1.20100000E+01 1.00800000E+00 1.00800000E+00 1.20100000E+01
1.00800000E+00
1.00800000E+00
%FLAG ATOM_TYPE_INDEX
%FORMAT(10I8)
1 2 2 1 2 2
%FLAG NUMBER_EXCLUDED_ATOMS
%FORMAT(10I8)
%FORMAT(10I8)
5 4 3 2 1 1
%FLAG NONBONDED_PARM_INDEX
%FORMAT(10I8)
1 2 2 3
%FLAG RESIDUE_LABEL
%FORMAT(20a4)
eth
%FLAG RESIDUE_POINTER
%FORMAT(10I8)
1
%FLAG BOND_FORCE_CONSTANT
%FORMAT(5E16.8)
3.54500000E+02 5.97700000E+02
%FLAG BOND_EQUIL_VALUE
%FORMAT(5E16.8)
1.08000000E+00 1.32000000E+00
%FLAG ANGLE_FORCE_CONSTANT
%FORMAT(5E16.8)
5.00000000E+01 3.81000000E+01
%FLAG ANGLE_EQUIL_VALUE
%FORMAT(5E16.8)
2.08916001E+00 2.07554644E+00
%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)
6.65000000E+00
%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8)
2.00000000E+00
%FLAG DIHEDRAL_PHASE
%FORMAT(5E16.8)
3.14159400E+00
%FLAG SOLTY
%FORMAT(5E16.8)
0.00000000E+00 0.00000000E+00
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
8.19971662E+05 8.61541883E+04 7.51607703E+03
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
5.31102864E+02 1.12529845E+02 2.17257828E+01
%FLAG BONDS_INC_HYDROGEN
%FORMAT(10I8)
0 3 1 0 6 1 9 12 1
9
15 1
%FLAG BONDS_WITHOUT_HYDROGEN
%FORMAT(10I8)
0 9 2
%FLAG ANGLES_INC_HYDROGEN
%FORMAT(10I8)
0 9 12 1 0 9 15 1 3
0
6 2 3 0 9 1 6 0 9
1
12 9 15 2
%FLAG ANGLES_WITHOUT_HYDROGEN
%FORMAT(10I8)
%FLAG DIHEDRALS_INC_HYDROGEN
%FORMAT(10I8)
3 0 9 12 1 3 0 9 15
1
6 0 9 12 1 6 0 9 15
1
%FLAG DIHEDRALS_WITHOUT_HYDROGEN
%FORMAT(10I8)
%FLAG EXCLUDED_ATOMS_LIST
%FORMAT(10I8)
2 3 4 5 6 3 4 5 6
4
5 6 5 6 6 0
%FLAG HBOND_ACOEF
%FORMAT(5E16.8)
%FLAG HBOND_BCOEF
%FORMAT(5E16.8)
%FLAG HBCUT
%FORMAT(5E16.8)
%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
c2 hc hc c2 hc hc
%FLAG TREE_CHAIN_CLASSIFICATION
%FORMAT(20a4)
M E E M E E
%FLAG JOIN_ARRAY
%FORMAT(10I8)
0 0 0 0 0 0
%FLAG IROTAT
%FORMAT(10I8)
0 0 0 0 0 0
%FLAG RADII
%FORMAT(5E16.8)
1.70000000E+00 1.20000000E+00 1.20000000E+00 1.70000000E+00
1.20000000E+00
1.20000000E+00
%FLAG SCREEN
%FORMAT(5E16.8)
7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
8.50000000E-01
8.50000000E-01
Now, I put nmode to run as follows
nmode -O -i nmdin -o nmdout -p eth.top -c eth.crd -v vectors &
where this is nmdin
Pentamer of Polystyrene
&data
ntrun = 1 ,
ibelly = 0 ,
maxcyc = 1 ,
drms = 50. ,
nvect = 5 ,
nsave = 10 ,
nprint = 1 ,
ivform = 1 ,
ntx = 1 ,
ntxo = 1 ,
&end
(the title is incorrect). After a few seconds I get the file nmdout
more nmdout
*******************************************************
Initiate the NMODE module of AMBER 7
*******************************************************
Pentamer of Polystyrene
ntrun maxcyc ibelly drms
1 1 0 0.50E+02
rcut scnb scee dielc idiel
99.00000 2.00000 2.00000 1.00000 0
nsave dfpred bdwnhl smx emx alpha ndiag
10 0.01000 0.10000 0.08000 0.30000 0.80000 10
ipol = 0
i3bod = 0
nvect = 5
| New format PARM file being parsed.
| Version = 1.000 Date = 07/01/03 Time = 15:48:48
PARM file has the title:
eth
Memory allocation :
1 7 13 15 17
19 21 23 25 27
28 29 30 32 35
38 38 38 38 62
0 1 7 14 21
26 27 30 35 40
45 47 49 51 58
65 72 79 80 81
82 83 488 893 1298
1703 2108 2513 2918 3323
3728 4133 4150 4156 4176
4190 4197 86 104 140
4204 0 4211 0 0
0 0 0 0 4162
4169 80 0
Duplicated 0 dihedrals
Duplicated 0 dihedrals
Memory allocation :
1 7 13 15 17
19 21 23 25 27
28 29 30 32 35
38 38 38 38 62
0 1 7 14 21
26 27 30 35 40
45 47 49 51 58
65 72 79 80 81
82 83 488 893 1298
1703 2108 2513 2918 3323
3728 4133 4150 4156 4176
4190 4197 86 104 140
4211 318 4218 319 481
499 0 0 0 4162
4169 80 0
Total memory required : 823 real words
Total memory avail : 3500000 real words
Total memory required : 4218 integer words
Total memory avail : 4000000 integer words
Maximum nonbond pairs 3995781
Getting coordinates from file with title:
eth
Number of non-bonded pairs = 0
Number of H-bonded pairs = 0
***************** ***************** *****************
step = 0
F = 0.109448E+02 GRDMAX = 0.942776E+02 GNORM = 0.414205E+02
E-NONB E-ELE E-HBOND E-BOND
0.00000E+00 0.00000E+00 0.00000E+00
0.96138E+01
E-ANGLE E-DIHED E-NB14 E-EEL14
0.32973E-01 0.15370E-09 0.12064E+00
0.11774E+01
E-POL E-3BOD
0.00000E+00 0.00000E+00
And that is it. Nmode keeps running but no more output even after one day
of running it. Did I do anything wrong or is nmode just way slow even for
molecules with 6 atoms ?. Thanks for your comments.
Gus Carri
Received on Tue Jul 01 2003 - 22:53:01 PDT
