Dear list,
I am trying to study solvent effects on an electrostatic protein.
I have a structure I obtained, and I have done simulations on
this thing out to ns using SHAKE. But I want to look at some
simulations without SHAKE (i.e., setting ntc=1).
I simply cannot seem to run sander successfully with ntc=1. I've
already equilibrated this protein under NPT conditions out to 0.250 ns
using SHAKE, yet I still keep failing because of problems with
exceeding the vlimit. I've tried time-steps as short as 0.1
fs. Nothing seems to stabilize the calculation.
I can definitely calculate this same kind of simulation on Discover
(Amber 6) with comparable conditions (below). I want to check these
Discover results using TIP3P water and amber7. What am I doing wrong?
Here is the complete AMBER7 output and the stderr output is also
listed at the end. (A minor note: I don't know why this was run in
1952, maybe I've suffered from an AIX/ENIAC twin-paradox.)
------------------------------------------
-------------------------------------------------------
Amber 7 SANDER Scripps/UCSF 2002
-------------------------------------------------------
| Run on Tue Apr 15 00:27:43 1952
[-O]verwriting output
File Assignments:
| MDIN: md2-ntc1.in
| MDOUT: test_Boxmdx1.out
|INPCRD: test_Boxmdx0.rst
| PARM: test_Box.top
|RESTRT: test_Boxmdx1.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: test_Boxmdx1.mden
| MDCRD: test_Boxmdx1.mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
MD simulation, 10 ps
&cntrl
imin=0, irest=1, ntx=5,
nstlim=1000,
nmropt=1,
ntwr=200,
ntwe=100,
ntwx=100,
ntpr=10,
dt=0.00025,
ntt=1,
ntp=1,
pres0=1.015,
cut=15.0,
ntb=2,
ntc=1,
ntf=2,
vlimit=20,
tempi=310.0,
temp0=310.0,
tautp=1.0,
/
&ewald
eedmeth=1,
/
&wt type='END'
/
DISANG=RST
#
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MEM_ALLOC MPI RLE ROWAT
getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
| New format PARM file being parsed.
| Version = 1.000 Date = 11/25/03 Time = 15:27:54
NATOM = 17461 NTYPES = 18 NBONH = 17032 MBONA = 436
NTHETH = 913 MTHETA = 590 NPHIH = 1745 MPHIA = 1092
NHPARM = 0 NPARM = 0 NNB = 26713 NRES = 5602
NBONA = 436 NTHETA = 590 NPHIA = 1092 NUMBND = 42
NUMANG = 86 NPTRA = 39 NATYP = 31 NPHB = 1
IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
| Memory Use Allocated
| Real 1258602
| Hollerith 110370
| Integer 862094
| Max Pairs 6127563
| Max Rstack 2000000
| Max Istack 2000000
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 0, nmropt = 1
Nature and format of input:
ntx = 5, irest = 1, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 10, ntrx = 1, ntwr = 200
iwrap = 0, ntwx = 100, ntwv = 0, ntwe = 100
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 2, ntb = 2, igb = 0, nsnb = 25
ipol = 0, gbsa = 0
dielc = 1.00000, cut = 15.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 1000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00025, vlimit = 20.00000
Temperature regulation:
ig = 71277, ntt = 1, vrand = 0
temp0 = 310.00000, tempi = 310.00000, heat = 0.00000
dtemp = 5.00000, tautp = 1.00000
Pressure regulation:
ntp = 1, plevel = 1
pres0 = 1.01500, comp = 44.60000, taup = 0.20000
NMR refinement options:
iscale = 0, noeskp = 1, ipnlty = 1, mxcub = 1
scalm = 100.00000, pencut = 0.10000, tausw = 0.10000
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, frc_int = 0, netfrc = 1
Box X = 55.892 Box Y = 56.422 Box Z = 56.350
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 60 NFFT2 = 60 NFFT3 = 60
Cutoff= 15.000 Tol =0.100E-04
Ewald Coefficient = 0.17871
Interpolation order = 4
| PLEVEL = 1: runmd parallelization, no EKCMR
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 232.600 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
** No weight changes given **
RESTRAINTS:
Requested file redirections:
DISANG = RST
Restraints will be read from file: RST
Here are comments from the DISANG input file:
#
# 25 CYS SG 30 CYS SG 2.8 3.2
Number of restraints read = 1
Done reading weight changes/NMR restraints
| Reorder water Setup:
| ----- Reordering water will NOT be done
| NMROPT not equal 0
|
Number of triangulated 3-point waters found: 5542
| Atom division among processors:
| 0 4366 8731 13096 17461
| Running AMBER/MPI version on 4 nodes
Sum of charges from parm topology file = -0.00000005
Forcing neutrality...
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.3388E-14 at 2.505100
| CHECK d/dx switch(x): max rel err = 0.7986E-11 at 2.679240
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 4496835
| TOTAL SIZE OF NONBOND LIST = 17628514
NSTEP = 10 TIME(PS) = 232.602 TEMP(K) = 298.10 PRESS = -2185.8
Etot = -42809.5148 EKtot = 15514.4310 EPtot = -58323.9458
BOND = 204.2093 ANGLE = 520.6311 DIHED = 530.3931
1-4 NB = 181.2874 1-4 EEL = 2788.4967 VDWAALS = 7116.6741
EELEC = -69666.2954 EHBOND = 0.0000 RESTRAINT = 0.6579
EAMBER (non-restraint) = -58324.6037
EKCMT = 5095.8433 VIRIAL = 13479.5162 VOLUME = 177644.1534
Density = 0.9913
Ewald error estimate: 0.6407E-05
------------------------------------------------------------------------------
===============================================================================
NMR restraints for step 10
Energy (this step): Bond = 0.658 Angle = 0.000 Torsion = 0.000
Energy (tot. run) : Bond = 0.662 Angle = 0.000 Torsion = 0.000
DEVIATIONS: Target=(r2+r3)/2 Target = closer of r2/r3
This step Entire run This step Entire run
ave. rms ave. rms ave. rms ave. rms
Bond 0.779 0.779 0.781 0.781 0.579 0.579 0.581 0.581
Angle 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
Torsion 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
===============================================================================
NSTEP = 20 TIME(PS) = 232.605 TEMP(K) = 627.70 PRESS =-10173.1
Etot = -42878.7961 EKtot = 32668.2956 EPtot = -75547.0917
BOND = 191.8645 ANGLE = 501.2709 DIHED = 529.0825
1-4 NB = 181.3232 1-4 EEL = 2782.9497 VDWAALS = 7302.6889
EELEC = -87036.9179 EHBOND = 0.0000 RESTRAINT = 0.6465
EAMBER (non-restraint) = -75547.7382
EKCMT = 5075.0875 VIRIAL = 43981.8937 VOLUME = 177130.4398
Density = 0.9941
Ewald error estimate: 0.8882E-05
------------------------------------------------------------------------------
===============================================================================
NMR restraints for step 20
Energy (this step): Bond = 0.646 Angle = 0.000 Torsion = 0.000
Energy (tot. run) : Bond = 0.657 Angle = 0.000 Torsion = 0.000
DEVIATIONS: Target=(r2+r3)/2 Target = closer of r2/r3
This step Entire run This step Entire run
ave. rms ave. rms ave. rms ave. rms
Bond 0.773 0.773 0.778 0.778 0.573 0.573 0.578 0.578
Angle 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
Torsion 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
===============================================================================
NSTEP = 30 TIME(PS) = 232.607 TEMP(K) = 1369.17 PRESS =-28768.3
Etot = -43463.4825 EKtot = 71258.0206 EPtot = -114721.5031
BOND = 166.7530 ANGLE = 443.3562 DIHED = 522.7411
1-4 NB = 179.4392 1-4 EEL = 2778.0989 VDWAALS = 7972.7864
EELEC = -126785.3098 EHBOND = 0.0000 RESTRAINT = 0.6319
EAMBER (non-restraint) = -114722.1351
EKCMT = 5078.1413 VIRIAL = 114047.4140 VOLUME = 175433.4875
Density = 1.0038
Ewald error estimate: 0.5301E-04
------------------------------------------------------------------------------
===============================================================================
NMR restraints for step 30
Energy (this step): Bond = 0.632 Angle = 0.000 Torsion = 0.000
Energy (tot. run) : Bond = 0.651 Angle = 0.000 Torsion = 0.000
DEVIATIONS: Target=(r2+r3)/2 Target = closer of r2/r3
This step Entire run This step Entire run
ave. rms ave. rms ave. rms ave. rms
Bond 0.766 0.766 0.775 0.775 0.566 0.566 0.575 0.575
Angle 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
Torsion 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
===============================================================================
NSTEP = 40 TIME(PS) = 232.610 TEMP(K) = 3142.52 PRESS =-81131.9
Etot = -47182.2867 EKtot = 163551.1041 EPtot = -210733.3908
BOND = 167.3398 ANGLE = 423.6836 DIHED = 514.9278
1-4 NB = 178.1821 1-4 EEL = 2777.0986 VDWAALS = 10130.2256
EELEC = -224925.4634 EHBOND = 0.0000 RESTRAINT = 0.6152
EAMBER (non-restraint) = -210734.0060
EKCMT = 5474.8584 VIRIAL = 304847.4455 VOLUME = 170900.1706
Density = 1.0304
Ewald error estimate: 0.2535E-04
------------------------------------------------------------------------------
===============================================================================
NMR restraints for step 40
Energy (this step): Bond = 0.615 Angle = 0.000 Torsion = 0.000
Energy (tot. run) : Bond = 0.644 Angle = 0.000 Torsion = 0.000
DEVIATIONS: Target=(r2+r3)/2 Target = closer of r2/r3
This step Entire run This step Entire run
ave. rms ave. rms ave. rms ave. rms
Bond 0.758 0.758 0.772 0.772 0.558 0.558 0.572 0.572
Angle 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
Torsion 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
===============================================================================
vlimit exceeded for step 42 ; vmax = 27.5954012646802589
vlimit exceeded for step 43 ; vmax = 138.959560144215487
vlimit exceeded for step 44 ; vmax = 119.776795686669814
vlimit exceeded for step 45 ; vmax = 165.223684329653508
vlimit exceeded for step 46 ; vmax = 180.570936430453798
vlimit exceeded for step 47 ; vmax = 229.954197612266995
vlimit exceeded for step 48 ; vmax = 749.379462585204124
vlimit exceeded for step 49 ; vmax = 809.343960320155134
NSTEP = 50 TIME(PS) = 232.612 TEMP(K) =100064.41 PRESS =********
Etot = 4290807.7799 EKtot = 5207807.0642 EPtot = -916999.2843
BOND = 179.1112 ANGLE = 452.0682 DIHED = 509.5124
1-4 NB = 178.7702 1-4 EEL = 2779.2682 VDWAALS = 23717.5414
EELEC = -944816.1529 EHBOND = 0.0000 RESTRAINT = 0.5969
EAMBER (non-restraint) = -916999.8813
EKCMT = 225135.2696 VIRIAL = 1273894.2971 VOLUME = 156000.2398
Density = 1.1288
Ewald error estimate: 0.1103E-04
------------------------------------------------------------------------------
===============================================================================
NMR restraints for step 50
Energy (this step): Bond = 0.597 Angle = 0.000 Torsion = 0.000
Energy (tot. run) : Bond = 0.636 Angle = 0.000 Torsion = 0.000
DEVIATIONS: Target=(r2+r3)/2 Target = closer of r2/r3
This step Entire run This step Entire run
ave. rms ave. rms ave. rms ave. rms
Bond 0.748 0.748 0.768 0.768 0.548 0.548 0.568 0.568
Angle 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
Torsion 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
===============================================================================
vlimit exceeded for step 50 ; vmax = 698.993868856018707
vlimit exceeded for step 51 ; vmax = 414.910311906575089
vlimit exceeded for step 52 ; vmax = 1628.37707913765939
vlimit exceeded for step 53 ; vmax = 1547.51242049349730
vlimit exceeded for step 54 ; vmax = 2698.52571209905454
vlimit exceeded for step 55 ; vmax = 2696.23180467852671
vlimit exceeded for step 56 ; vmax = 2295.21036036854639
vlimit exceeded for step 57 ; vmax = 3185.33984517002500
vlimit exceeded for step 58 ; vmax = 4707.94695676927222
vlimit exceeded for step 59 ; vmax = 1693.37577817678016
NSTEP = 60 TIME(PS) = 232.615 TEMP(K) =227552.14 PRESS =********
Etot = 9367982.8928 EKtot = ************ EPtot = ************
BOND = 620.6349 ANGLE = 677.5709 DIHED = 552.3036
1-4 NB = 185.8595 1-4 EEL = 2781.7005 VDWAALS = 64956.2605
EELEC = ************ EHBOND = 0.0000 RESTRAINT = 0.5781
EAMBER (non-restraint) = ************
EKCMT = 3048945.8319 VIRIAL = 5276292.3048 VOLUME = 165545.6053
Density = 1.0637
Ewald error estimate: 0.2075E-05
------------------------------------------------------------------------------
===============================================================================
NMR restraints for step 60
Energy (this step): Bond = 0.578 Angle = 0.000 Torsion = 0.000
Energy (tot. run) : Bond = 0.628 Angle = 0.000 Torsion = 0.000
DEVIATIONS: Target=(r2+r3)/2 Target = closer of r2/r3
This step Entire run This step Entire run
ave. rms ave. rms ave. rms ave. rms
Bond 0.739 0.739 0.764 0.764 0.539 0.539 0.564 0.564
Angle 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
Torsion 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
===============================================================================
vlimit exceeded for step 60 ; vmax = 1823.84265923123826
vlimit exceeded for step 61 ; vmax = 525.756187843766384
vlimit exceeded for step 62 ; vmax = 2541.60983804967918
vlimit exceeded for step 63 ; vmax = 925.816197967856510
EWALD BOMB in subroutine ewald_list
volume of ucell too big, too many subcells
list grid memory needs to be reallocated, restart sander
********************************************
********************************************
Here is the stderr output:
------------------------------
AIX 224% EWALD BOMB in subroutine ewald_list
volume of ucell too big, too many subcells
list grid memory needs to be reallocated, restart sander
EWALD BOMB in subroutine ewald_list
EWALD BOMB in subroutine ewald_list
volume of ucell too big, too many subcells
list grid memory needs to be reallocated, restart sander
volume of ucell too big, too many subcells
list grid memory needs to be reallocated, restart sander
ERROR: 0031-250 task 0: Terminated
ERROR: 0031-250 task 1: Terminated
ERROR: 0031-250 task 2: Terminated
ERROR: 0031-250 task 3: Terminated
********************************************
********************************************
Thank you,
Sincerely
Wayne
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Received on Wed Jan 14 2004 - 15:53:11 PST
