Dear All
I am trying to use nudged elastic band method (NEB) to calculate the
lowest energy path between two conformations of a 234-atom molecule.
This will help choose a suitable reaction coordinate for umbrella
sampling . I followed the tutorial on NEB
(
http://amber.scripps.edu/tutorials/advanced/tutorial5/index.htm). The
only difference is that I am using my molecule and the gaff forcefield
and I ran the calculation in vacuum, not in implicit solvent as the
tutorial does. When I checked the output of the initial heating MD, the
potential enery and VDW were listed as NaN and the atomic velocities and
individual replicate energies were ****. Please see the output below.
Any suggestions on what I might have done wrong would be much
appreciated
Many thanks
Mike
-------------------------------------------------------
Amber 9 SANDER 2006
-------------------------------------------------------
| Run on 01/07/2008 at 15:38:23
[-O]verwriting output
File Assignments:
| MDIN: md_neb_smallk_1.in
| MDOUT: md_neb_smallk_1.out
|INPCRD: neb.inpcrd
| PARM: neb.prmtop
|RESTRT: md_neb_smallk_1.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: md_neb_smallk_1.mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
o2o NEB initial MD with small K
&cntrl
imin = 0, irest = 0,
ntc=1, ntf=1,
ntpr=50, ntwx=500,
ntb = 0, cut = 999.0, rgbmax=999.0,
nstlim = 40000, nscm=0,
dt = 0.0005,
ntt = 3, gamma_ln=1000.0,
tempi=0, temp0=300,
ineb = 1,skmin = 10,skmax = 10,
nmropt=1
/
&wt type='TEMP0', istep1=0,istep2=35000,
value1=0.0, value2=300.0
/
&wt type='END'
/
------------------------------------------------------------------------
--------
1. RESOURCE USE:
------------------------------------------------------------------------
--------
| Flags: PIMD
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
| *** cutoff > system size, list only builds once
|Largest sphere to fit in unit cell has radius = 43.803
NATOM = 7020 NTYPES = 8 NBONH = 3240 MBONA = 4320
NTHETH = 7380 MTHETA = 6420 NPHIH = 11700 MPHIA = 11880
NHPARM = 0 NPARM = 1 NNB = 40740 NRES = 1
NBONA = 4320 NTHETA = 6420 NPHIA = 11880 NUMBND = 26
NUMANG = 48 NPTRA = 36 NATYP = 9 NPHB = 0
IFBOX = 0 NMXRS = 7020 IFCAP = 0 NEXTRA = 0
NCOPY = 30
| Memory Use Allocated
| Real 340550
| Hollerith 42123
| Integer 531596
| Max Pairs 24636690
| nblistReal 84240
| nblist Int 3157235
| Total 114129 kbytes
LES parameters were found
0 LES atom pairs require adjustment
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
------------------------------------------------------------------------
--------
2. CONTROL DATA FOR THE RUN
------------------------------------------------------------------------
--------
UNK
General flags:
imin = 0, nmropt = 1
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 50, ntrx = 1, ntwr =
500
iwrap = 0, ntwx = 500, ntwv = 0, ntwe =
0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
0
Potential function:
ntf = 1, ntb = 0, igb = 0, nsnb =
25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 40000, nscm = 999999999, nrespa = 1
t = 0.00000, dt = 0.00050, vlimit = 20.00000
Langevin dynamics temperature regulation:
ig = 71277
temp0 = 300.00000, tempi = 0.00000, gamma_ln=1000.00000
NMR refinement options:
iscale = 0, noeskp = 1, ipnlty = 1, mxsub =
1
scalm = 100.00000, pencut = 0.10000, tausw = 0.10000
| INFO: Old style inpcrd file read
------------------------------------------------------------------------
--------
3. ATOMIC COORDINATES AND VELOCITIES
------------------------------------------------------------------------
--------
UNK
begin time read from input coords = 0.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
TEMP0 0 35000 0.000000 300.000000 0 0
RESTRAINTS:
** No restraint defined **
Done reading weight changes/NMR restraints
Number of triangulated 3-point waters found: 0
Sum of charges from parm topology file = 0.00004000
Forcing neutrality...
------------------------------------------------------------------------
--------
4. RESULTS
------------------------------------------------------------------------
--------
THIS IS A PIMD RUN
PIMD parameters:
propagator & thermostat = Langevin (BBK)
number of beads = 30
number of classical atoms = 234
temperature (Kelvin) = 300.00
# degrees of freedom in non-LES region: 21060.
# degrees of freedom in LES region: 0.
---------------------------------------------------
eedmeth=4: Setting switch to one everywhere
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 24596190
| TOTAL SIZE OF NONBOND LIST = 24596190
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = NaN EKtot = 0.0000 EPtot = NaN
BOND = 314.1969 ANGLE = 785.4154 DIHED =
1469.4951
1-4 NB = 2915.1250 1-4 EEL = -7861.0498 VDWAALS = NaN
EELEC = Infinity EHBOND = 0.0000 RESTRAINT =
0.0000
NEB replicate breakdown:
Energy for replicate 1 = *************
Energy for replicate 2 = NaN
Energy for replicate 3 = NaN
Energy for replicate 4 = NaN
Energy for replicate 5 = NaN
Energy for replicate 6 = NaN
Energy for replicate 7 = NaN
Energy for replicate 8 = NaN
Energy for replicate 9 = NaN
Energy for replicate 10 = NaN
Energy for replicate 11 = NaN
Energy for replicate 12 = NaN
Energy for replicate 13 = NaN
Energy for replicate 14 = NaN
Energy for replicate 15 = NaN
Energy for replicate 16 = *************
Energy for replicate 17 = NaN
Energy for replicate 18 = NaN
Energy for replicate 19 = NaN
Energy for replicate 20 = NaN
Energy for replicate 21 = NaN
Energy for replicate 22 = NaN
Energy for replicate 23 = NaN
Energy for replicate 24 = NaN
Energy for replicate 25 = NaN
Energy for replicate 26 = NaN
Energy for replicate 27 = NaN
Energy for replicate 28 = NaN
Energy for replicate 29 = NaN
Energy for replicate 30 = NaN
Total Energy of replicates = NaN
NEB RMS = NaN
------------------------------------------------------------------------
------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
0.000
========================================================================
=======
vlimit exceeded for step 0; vmax = **********
vlimit exceeded for step 1; vmax = **********
vlimit exceeded for step 2; vmax = **********
vlimit exceeded for step 3; vmax = **********
vlimit exceeded for step 4; vmax = **********
vlimit exceeded for step 5; vmax = **********
vlimit exceeded for step 6; vmax = **********
vlimit exceeded for step 7; vmax = **********
vlimit exceeded for step 8; vmax = **********
vlimit exceeded for step 9; vmax = **********
vlimit exceeded for step 10; vmax = **********
vlimit exceeded for step 11; vmax = **********
vlimit exceeded for step 12; vmax = **********
vlimit exceeded for step 13; vmax = **********
vlimit exceeded for step 14; vmax = **********
vlimit exceeded for step 15; vmax = **********
vlimit exceeded for step 16; vmax = **********
vlimit exceeded for step 17; vmax = **********
vlimit exceeded for step 18; vmax = **********
vlimit exceeded for step 19; vmax = **********
vlimit exceeded for step 20; vmax = **********
vlimit exceeded for step 21; vmax = **********
vlimit exceeded for step 22; vmax = **********
vlimit exceeded for step 23; vmax = **********
vlimit exceeded for step 24; vmax = **********
vlimit exceeded for step 25; vmax = **********
vlimit exceeded for step 26; vmax = **********
vlimit exceeded for step 27; vmax = **********
vlimit exceeded for step 28; vmax = **********
vlimit exceeded for step 29; vmax = **********
vlimit exceeded for step 30; vmax = **********
vlimit exceeded for step 31; vmax = **********
vlimit exceeded for step 32; vmax = **********
vlimit exceeded for step 33; vmax = **********
vlimit exceeded for step 34; vmax = **********
vlimit exceeded for step 35; vmax = **********
vlimit exceeded for step 36; vmax = **********
vlimit exceeded for step 37; vmax = **********
vlimit exceeded for step 38; vmax = **********
vlimit exceeded for step 39; vmax = **********
vlimit exceeded for step 40; vmax = **********
vlimit exceeded for step 41; vmax = **********
vlimit exceeded for step 42; vmax = **********
vlimit exceeded for step 43; vmax = **********
vlimit exceeded for step 44; vmax = **********
vlimit exceeded for step 45; vmax = **********
vlimit exceeded for step 46; vmax = **********
vlimit exceeded for step 47; vmax = **********
vlimit exceeded for step 48; vmax = **********
vlimit exceeded for step 49; vmax = **********
And so on....
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Received on Wed Jan 09 2008 - 06:07:22 PST
