AMBER Archive (2008)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Jan 08 2008 - 17:00:59 CST


Hi Mike,

My initial guess would be that it is a problem with your initial structures
more than it is a problem with the NEB setup. Take your two end points and
run them as a standard gas phase simulation and see if you can run standard
MD on them. If you still get extremely large VDW or EELEC then I would look
carefully at the two structures and see if you can find where the problem
is. There is likely two atoms sitting on top of each other.

Did you minimize the two end points before you built the NEB input files?
You need to do this.

Good luck,
Ross

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Mike Wykes
> Sent: Tuesday, January 08, 2008 02:42
> To: amber_at_scripps.edu
> Subject: AMBER: Nudged Elastic Band initial heating problem
>
> 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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