AMBER Archive (2008)

Subject: Re: AMBER: Nudged Elastic Band initial heating problem

From: Keith Van Nostrand (kifvan_at_yahoo.com)
Date: Tue Jan 08 2008 - 07:32:31 CST

Mike,
   
    It could be your initial structures. Notice how Image 1 and image 16 are *** instead of NaN for the first step. You can test your input file with another structure to see if it works for that or gives the same behavior.
   
  Sincerely,
  Keith Van Nostrand

Mike Wykes <wykesm_at_averell.umh.ac.be> wrote:
  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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