I suspect this may be worth looking into:
Sum of charges from parm topology file = ************
Bill
On 8/14/19 1:53 PM, Parviz Seifpanahi Shabane wrote:
> Hi All,
> I have a very big system 660 K. When I run the system, I got "Segmentation
> Fault" error. I played with "min" script, changing "maxcyc, ntwx, ntwr".
> the simulation would run for 30 steps and then stop. I reduce " maxcyc" to
> 28 and ntwr=9, and still not working this (below) the file.mdout for
> minimization and "heat".
> How can I solve this problem?
>
> "Min" out put
> =======================================
> NFFT1 = 180 NFFT2 = 250 NFFT3 = 135
> Cutoff= 9.000 Tol =0.100E-04
> Ewald Coefficient = 0.30768
> Interpolation order = 4
>
> LOADING THE CONSTRAINED ATOMS AS GROUPS
>
>
> 5. REFERENCE ATOM COORDINATES
>
> defa
> ----- READING GROUP 1; TITLE:
> RESTRAIN ALL
>
>
> GROUP 1 HAS HARMONIC CONSTRAINTS 5.00000
> GRP 1 RES 1 TO 9999
> Number of atoms in this group = 60028
> ----- END OF GROUP READ -----
> | EXTRA_PTS, trim_bonds: num bonds BEFORE trim =494860 0
> | EXTRA_PTS, trim_bonds: num bonds AFTER trim =494860 0
> | EXTRA_PTS, trim_bonds: num bonds BEFORE trim =175551 0
> | EXTRA_PTS, trim_bonds: num bonds AFTER trim = 14430 0
> | EXTRA_PTS, trim_theta: num angle BEFORE trim = 26427 0
> | EXTRA_PTS, trim_theta: num angle AFTER trim = 26427 0
> | EXTRA_PTS, trim_theta: num angle BEFORE trim = 20681 0
> | EXTRA_PTS, trim_theta: num angle AFTER trim = 20681 0
> | EXTRA_PTS, trim_phi: num diheds BEFORE trim = 52213 0
> | EXTRA_PTS, trim_phi: num diheds AFTER trim = 52213 0
> | EXTRA_PTS, trim_phi: num diheds BEFORE trim = 44220 0
> | EXTRA_PTS, trim_phi: num diheds AFTER trim = 44220 0
>
> --------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
> --------------------------------------------------------------------------------
>
> default_name
>
> begin time read from input coords = 0.000 ps
>
> Number of triangulated 3-point waters found: 161121
>
> Sum of charges from parm topology file = ************
> Assuming uniform neutralizing plasma
>
> --------------------------------------------------------------------------------
> 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 = 0.3338E-14 at 2.509280
> | CHECK d/dx switch(x): max rel err = 0.8261E-11 at 2.768360
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 222730264
> | TOTAL SIZE OF NONBOND LIST = 222730264
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 9.6444E+06 1.9817E+02 2.3628E+05 N 14502
>
> BOND = 11548100.3201 ANGLE = 6025.3459 DIHED =
> 16671.4002
> VDWAALS = 260779.4630 EEL = -2201179.5517 HBOND =
> 0.0000
> 1-4 VDW = 7609.4364 1-4 EEL = 6393.5497 RESTRAINT =
> 0.0190
> EAMBER = 9644399.9636
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 2 9.6430E+06 1.9815E+02 2.3627E+05 N 14502
>
> BOND = 11546709.9753 ANGLE = 6025.0673 DIHED =
> 16671.3946
> VDWAALS = 260778.8861 EEL = -2201192.6131 HBOND =
> 0.0000
> 1-4 VDW = 7609.4238 1-4 EEL = 6393.5684 RESTRAINT =
> 0.0191
> EAMBER = 9642995.7025
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 3 9.6413E+06 1.9814E+02 2.3625E+05 N 14502
>
> BOND = 11545041.6758 ANGLE = 6024.7344 DIHED =
> 16671.3880
> VDWAALS = 260778.1953 EEL = -2201208.2872 HBOND =
> 0.0000
> 1-4 VDW = 7609.4088 1-4 EEL = 6393.5909 RESTRAINT =
> 0.0196
> EAMBER = 9641310.7059
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 4 9.6393E+06 1.9812E+02 2.3623E+05 N 14502
>
> BOND = 11543039.8813 ANGLE = 6024.3368 DIHED =
> 16671.3800
> VDWAALS = 260777.3651 EEL = -2201227.2317 HBOND =
> 0.0000
> 1-4 VDW = 7609.3908 1-4 EEL = 6393.6178 RESTRAINT =
> 0.0207
> EAMBER = 9639288.7401
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 5 9.6369E+06 1.9810E+02 2.3621E+05 N 14502
>
> BOND = 11540637.9651 ANGLE = 6023.8626 DIHED =
> 16671.3705
> VDWAALS = 260776.3691 EEL = -2201251.2933 HBOND =
> 0.0000
> 1-4 VDW = 7609.3695 1-4 EEL = 6393.6501 RESTRAINT =
> 0.0226
> EAMBER = 9636861.2937
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 6 9.6340E+06 1.9807E+02 2.3618E+05 N 14502
>
> BOND = 11537756.0075 ANGLE = 6023.2976 DIHED =
> 16671.3591
> VDWAALS = 260775.1738 EEL = -2201278.4202 HBOND =
> 0.0000
> 1-4 VDW = 7609.3442 1-4 EEL = 6393.6889 RESTRAINT =
> 0.0259
> EAMBER = 9633950.4510
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 7 9.6305E+06 1.9804E+02 2.3614E+05 N 14502
>
> BOND = 11534298.1506 ANGLE = 6022.6255 DIHED =
> 16671.3456
> VDWAALS = 260773.7412 EEL = -2201310.9399 HBOND =
> 0.0000
> 1-4 VDW = 7609.3143 1-4 EEL = 6393.7354 RESTRAINT =
> 0.0312
> EAMBER = 9630457.9726
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 8 9.6263E+06 1.9801E+02 2.3610E+05 N 14502
>
> BOND = 11530149.4310 ANGLE = 6021.8276 DIHED =
> 16671.3295
> VDWAALS = 260772.0244 EEL = -2201349.0438 HBOND =
> 0.0000
> 1-4 VDW = 7609.2789 1-4 EEL = 6393.7913 RESTRAINT =
> 0.0397
> EAMBER = 9626268.6388
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 9 9.6212E+06 1.9796E+02 2.3605E+05 N 14502
>
> BOND = 11525171.9883 ANGLE = 6020.8825 DIHED =
> 16671.3103
> VDWAALS = 260769.9655 EEL = -2201395.8656 HBOND =
> 0.0000
> 1-4 VDW = 7609.2373 1-4 EEL = 6393.8583 RESTRAINT =
> 0.0527
> EAMBER = 9621241.3766
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 10 9.6152E+06 1.9791E+02 2.3598E+05 N 14502
>
> BOND = 11519200.5271 ANGLE = 6019.7663 DIHED =
> 16671.2876
> VDWAALS = 260767.4958 EEL = -2201452.1151 HBOND =
> 0.0000
> 1-4 VDW = 7609.1886 1-4 EEL = 6393.9388 RESTRAINT =
> 0.0726
> EAMBER = 9615210.0890
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 11 9.6080E+06 1.9784E+02 2.3591E+05 N 14502
>
> BOND = 11512036.8909 ANGLE = 6018.4529 DIHED =
> 16671.2608
> VDWAALS = 260764.5366 EEL = -2201519.8225 HBOND =
> 0.0000
> 1-4 VDW = 7609.1318 1-4 EEL = 6394.0354 RESTRAINT =
> 0.1025
> EAMBER = 9607974.4858
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 12 9.6080E+06 1.9784E+02 2.3591E+05 N 14502
>
> BOND = 11512035.9009 ANGLE = 6018.4527 DIHED =
> 16671.2608
> VDWAALS = 260764.5362 EEL = -2201519.8319 HBOND =
> 0.0000
> 1-4 VDW = 7609.1318 1-4 EEL = 6394.0354 RESTRAINT =
> 0.1025
> EAMBER = 9607973.4858
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 13 3.7215E+06 2.2305E+02 1.6386E+05 N 14502
>
> BOND = 5651048.8710 ANGLE = 7109.0970 DIHED =
> 16676.9768
> VDWAALS = 297447.9050 EEL = -2267766.8539 HBOND =
> 0.0000
> 1-4 VDW = 7563.7912 1-4 EEL = 6254.3141 RESTRAINT =
> 3188.6567
> EAMBER = 3718334.1013
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 14 8.7660E+07 1.5088E+06 1.1301E+09 O 459333
>
> BOND = 2404567.1773 ANGLE = 7188.9953 DIHED =
> 16654.5595
> VDWAALS = 87534001.9216 EEL = -2327261.6827 HBOND =
> 0.0000
> 1-4 VDW = 7527.1600 1-4 EEL = 6169.9266 RESTRAINT =
> 11300.9233
> EAMBER = 87648848.0575
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 15 2.1600E+06 3.6809E+03 3.0215E+06 O 464113
>
> BOND = 3797746.2236 ANGLE = 7177.1593 DIHED =
> 16667.2481
> VDWAALS = 615481.1035 EEL = -2297424.3413 HBOND =
> 0.0000
> 1-4 VDW = 7545.3558 1-4 EEL = 6207.8195 RESTRAINT =
> 6623.8411
> EAMBER = 2153400.5686
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 16 1.1135E+06 6.9981E+02 6.4014E+05 H 14503
>
> BOND = 3043636.2491 ANGLE = 7187.3412 DIHED =
> 16661.2570
> VDWAALS = 335870.7632 EEL = -2312411.6156 HBOND =
> 0.0000
> 1-4 VDW = 7536.2226 1-4 EEL = 6188.2348 RESTRAINT =
> 8807.1450
> EAMBER = 1104668.4523
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 17 7.4014E+05 2.8513E+02 2.0639E+05 N 14502
>
> BOND = 2709721.2215 ANGLE = 7189.0682 DIHED =
> 16658.0079
> VDWAALS = 302734.6746 EEL = -2319891.1440 HBOND =
> 0.0000
> 1-4 VDW = 7531.6823 1-4 EEL = 6178.9512 RESTRAINT =
> 10015.2248
> EAMBER = 730122.4617
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 18 -2.7852E+05 2.1933E+03 1.7515E+06 CA 14504
>
> BOND = 1620256.1168 ANGLE = 7051.1694 DIHED =
> 16635.6168
> VDWAALS = 496921.3519 EEL = -2478871.9490 HBOND =
> 0.0000
> 1-4 VDW = 8200.1272 1-4 EEL = 6033.9272 RESTRAINT =
> 45252.3289
> EAMBER = -323773.6397
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 19 1.8754E+07 3.0706E+05 1.9968E+08 C5 895
>
> BOND = 1025354.8560 ANGLE = 6955.8834 DIHED =
> 16621.2199
> VDWAALS = 20066065.5276 EEL = -2398675.7787 HBOND =
> 0.0000
> 1-4 VDW = 7494.8779 1-4 EEL = 6105.4817 RESTRAINT =
> 24119.0555
> EAMBER = 18729922.0678
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 20 -9.4332E+05 8.7161E+02 5.9617E+05 CA 14504
>
> BOND = 1047650.1499 ANGLE = 6687.3231 DIHED =
> 16633.1870
> VDWAALS = 377099.9185 EEL = -2438807.4022 HBOND =
> 0.0000
> 1-4 VDW = 7536.6792 1-4 EEL = 6069.8307 RESTRAINT =
> 33807.0117
> EAMBER = -977130.3138
>
>
> Maximum number of minimization cycles reached.
>
>
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 20 -9.4332E+05 8.7161E+02 5.9617E+05 CA 14504
>
> BOND = 1047650.1499 ANGLE = 6687.3231 DIHED =
> 16633.1870
> VDWAALS = 377099.9185 EEL = -2438807.4382 HBOND =
> 0.0000
> 1-4 VDW = 7536.6792 1-4 EEL = 6069.8307 RESTRAINT =
> 33807.0117
> EAMBER = -977130.3498
>
> --------------------------------------------------------------------------------
> 5. TIMINGS
> --------------------------------------------------------------------------------
>
> | Read coords time 0.47 ( 0.31% of Total)
> | Fast Water setup 0.01 ( 0.01% of Total)
> | Build the list 56.33 (99.79% of List )
> | Other 0.12 ( 0.21% of List )
> | List time 56.45 (38.31% of Nonbo)
> | Short_ene time 76.87 (98.71% of Direc)
> | Other 1.00 ( 1.29% of Direc)
> | Direct Ewald time 77.87 (85.66% of Ewald)
> | Adjust Ewald time 0.49 ( 0.54% of Ewald)
> | Fill Bspline coeffs 0.60 ( 4.95% of Recip)
> | Fill charge grid 1.84 (15.13% of Recip)
> | Scalar sum 1.81 (14.90% of Recip)
> | Grad sum 3.35 (27.54% of Recip)
> | FFT time 4.56 (37.49% of Recip)
> | Recip Ewald time 12.16 (13.37% of Ewald)
> | Virial junk 0.05 ( 0.06% of Ewald)
> | Other 0.34 ( 0.37% of Ewald)
> | Ewald time 90.91 (61.69% of Nonbo)
> | Nonbond force 147.36 (99.55% of Force)
> | Bond/Angle/Dihedral 0.63 ( 0.43% of Force)
> | Other 0.04 ( 0.03% of Force)
> | Force time 148.04 (100.0% of Runmd)
> | Runmd Time 148.04 (96.43% of Total)
> | Other 5.00 ( 3.26% of Total)
> | Total time 153.52 (100.0% of ALL )
>
> | Number of list builds : 10
>
> | Highest rstack allocated: 30549614
> | Highest istack allocated: 669588
> | Job began at 16:24:23.812 on 08/14/2019
> | Setup done at 16:24:28.018 on 08/14/2019
> | Run done at 16:26:57.333 on 08/14/2019
> | wallclock() was called 828 times
>
> |3D-RISM memory allocation summary
> |Type Maximum Current
> |Integer 0.00000 GB 0.00000 GB
> |Real 0.00000 GB 0.00000 GB
> |Logical 0.00000 GB 0.00000 GB
> |Character 0.00000 GB 0.00000 GB
> |---------------------------------------
> |Total 0.00000 GB 0.00000 GB
> ================================================
> "heat" out put
>
> ================================================
> -------------------------------------------------------
> Amber 18 PMEMD 2018
> -------------------------------------------------------
>
> | PMEMD implementation of SANDER, Release 18
>
> | Run on 08/14/2019 at 16:26:57
>
> | Executable path:
> /home/sparviz/cascades/Amber/amber18/bin/pmemd.cuda_SPFP
> | Working directory: /home/sparviz/cascades/1KX5-KCl-iodFF
> | Hostname: ca198
>
> [-O]verwriting output
>
> File Assignments:
> | MDIN: heat.pme.mdin
>
> | MDOUT: 1KX5-ED25A-iodFF-KCL.heat.mdout
>
> | INPCRD: 1KX5-ED25A-iodFF-KCL.min.restrt
>
> | PARM: 1KX5-ED25A-iodFF-KCL.top
>
> | RESTRT: 1KX5-ED25A-iodFF-KCL.heat.restrt
>
> | REFC: 1KX5-ED25A-iodFF-KCL.crd
>
> | MDVEL: mdvel
>
> | MDEN: mden
>
> | MDCRD: mdcrd
>
> | MDINFO: mdinfo
>
> | MDFRC: mdfrc
>
>
>
> Here is the input file:
>
> NVT: Heat to 300K over 600ps, shake (ntc=2,ntf=2), langevin (ntt=3)
>
> &cntrl
>
> imin=0, ! MD, not mimimization
>
> ig=-1, ! random seed based on date/time
>
> nstlim=600000, ! n steps of MD
>
> dt=0.002, ! time step (ps)
>
> ntc=2, ! shake: constrain H bonds
>
> ntf=2, ! shake: ignore H bond interactions
>
> ntt=3, ! 3 = langevin dynamics
>
> gamma_ln=1, ! collision frequency for langevin dynamics
>
> tempi=0.0, ! initial temperature
>
> temp0=300.0, ! reference temperature
>
> ntp=0, ! no pressure scaling (const volume)
>
> ntb=1, ! periodic boundary for const volume md
>
> igb=0, ! pme
>
> cut=9.0, ! cutoff for electrostatics
>
> ntr=1, ! use restraints
>
> ntx=1, ! input: formatted coord only
>
> irest=0, ! input: not a restart
>
> ntpr=500, ! output: print every n steps
>
> ntwe=0, ! output: do not write energy and temperature file
>
> ntwx=0, ! output: no trajectory
>
> ntwprt=0, ! output: n atoms written to traj (0=all atoms)
>
> ntwr=1000, ! output: restart file written every n steps
>
> iwrap=0, ! output: do not wrap coord in restart/traj (for pme)
>
> /
>
> RESTRAIN ALL
>
> 1.0
>
> RES 1 9999
>
> END
>
> END
>
>
>
>
>
>
>
> Note: ig = -1. Setting random seed to 395413 based on wallclock time in
> microseconds.
> | irandom = 1, using AMBER's internal random number generator (default).
>
> |--------------------- INFORMATION ----------------------
> | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
> | Version 18.0.0
> |
> | 03/25/2018
> |
> | Implementation by:
> | Ross C. Walker (SDSC)
> | Scott Le Grand (nVIDIA)
> |
> | Version 18 performance extensions by:
> | David Cerutti (Rutgers)
> |
> | Precision model in use:
> | [SPFP] - Single Precision Forces, 64-bit Fixed Point
> | Accumulation. (Default)
> |
> |--------------------------------------------------------
>
> |----------------- CITATION INFORMATION -----------------
> |
> | When publishing work that utilized the CUDA version
> | of AMBER, please cite the following in addition to
> | the regular AMBER citations:
> |
> | - Romelia Salomon-Ferrer; Andreas W. Goetz; Duncan
> | Poole; Scott Le Grand; Ross C. Walker "Routine
> | microsecond molecular dynamics simulations with
> | AMBER - Part II: Particle Mesh Ewald", J. Chem.
> | Theory Comput., 2013, 9 (9), pp3878-3888,
> | DOI: 10.1021/ct400314y.
> |
> | - Andreas W. Goetz; Mark J. Williamson; Dong Xu;
> | Duncan Poole; Scott Le Grand; Ross C. Walker
> | "Routine microsecond molecular dynamics simulations
> | with AMBER - Part I: Generalized Born", J. Chem.
> | Theory Comput., 2012, 8 (5), pp1542-1555.
> |
> | - Scott Le Grand; Andreas W. Goetz; Ross C. Walker
> | "SPFP: Speed without compromise - a mixed precision
> | model for GPU accelerated molecular dynamics
> | simulations.", Comp. Phys. Comm., 2013, 184
> | pp374-380, DOI: 10.1016/j.cpc.2012.09.022
> |
> |--------------------------------------------------------
>
> |------------------- GPU DEVICE INFO --------------------
> |
> | CUDA_VISIBLE_DEVICES: 0
> | CUDA Capable Devices Detected: 1
> | CUDA Device ID in use: 0
> | CUDA Device Name: Tesla V100-PCIE-16GB
> | CUDA Device Global Mem Size: 16130 MB
> | CUDA Device Num Multiprocessors: 80
> | CUDA Device Core Freq: 1.38 GHz
> |
> |--------------------------------------------------------
>
>
> | Conditional Compilation Defines Used:
> | PUBFFT
> | BINTRAJ
> | CUDA
> | EMIL
>
> | Largest sphere to fit in unit cell has radius = 65.029
>
> | New format PARM file being parsed.
> | Version = 1.000 Date = 08/14/19 Time = 13:46:44
>
> | Note: 1-4 EEL scale factors are being read from the topology file.
>
> | Note: 1-4 VDW scale factors are being read from the topology file.
> | Duplicated 0 dihedrals
>
> | Duplicated 0 dihedrals
>
> --------------------------------------------------------------------------------
> 1. RESOURCE USE:
> --------------------------------------------------------------------------------
>
> getting box info from netcdf restart file
> NATOM = 669588 NTYPES = 20 NBONH = 494860 MBONA = 175551
> NTHETH = 26427 MTHETA = 20681 NPHIH = 52213 MPHIA = 44220
> NHPARM = 0 NPARM = 0 NNB = 1266828 NRES = 162389
> NBONA = 175551 NTHETA = 20681 NPHIA = 44220 NUMBND = 64
> NUMANG = 136 NPTRA = 64 NATYP = 37 NPHB = 1
> IFBOX = 1 NMXRS = 33 IFCAP = 0 NEXTRA = 161121
> NCOPY = 0
>
> | Coordinate Index Table dimensions: 35 48 26
> | Direct force subcell size = 5.1347 5.0878 5.0022
>
> BOX TYPE: RECTILINEAR
>
> --------------------------------------------------------------------------------
> 2. CONTROL DATA FOR THE RUN
> --------------------------------------------------------------------------------
>
> default_name
>
>
> General flags:
> imin = 0, nmropt = 0
>
> Nature and format of input:
> ntx = 1, irest = 0, ntrx = 1
>
> Nature and format of output:
> ntxo = 2, ntpr = 500, ntrx = 1, ntwr =
> 1000
> iwrap = 0, ntwx = 0, ntwv = 0, ntwe =
> 0
> ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat=
> 0
>
> Potential function:
> ntf = 2, ntb = 1, igb = 0, nsnb =
> 25
> ipol = 0, gbsa = 0, iesp = 0
> dielc = 1.00000, cut = 9.00000, intdiel = 1.00000
>
> Frozen or restrained atoms:
> ibelly = 0, ntr = 1
> restraint_wt = 0.00000
>
> Molecular dynamics:
> nstlim = 600000, nscm = 0, nrespa = 1
> t = 0.00000, dt = 0.00200, vlimit = -1.00000
>
> Langevin dynamics temperature regulation:
> ig = 395413
> temp0 = 300.00000, tempi = 0.00000, gamma_ln= 1.00000
>
> SHAKE:
> ntc = 2, jfastw = 0
> tol = 0.00001
>
> | Intermolecular bonds treatment:
> | no_intermolecular_bonds = 1
>
> | Energy averages sample interval:
> | ene_avg_sampling = 500
>
> Extra-points options:
> frameon = 1, chngmask= 1
>
> Ewald parameters:
> verbose = 0, ew_type = 0, nbflag = 1, use_pme =
> 1
> vdwmeth = 1, eedmeth = 1, netfrc = 1
> Box X = 179.713 Box Y = 244.216 Box Z = 130.058
> Alpha = 90.000 Beta = 90.000 Gamma = 90.000
> NFFT1 = 180 NFFT2 = 256 NFFT3 = 128
> Cutoff= 9.000 Tol =0.100E-04
> Ewald Coefficient = 0.30768
> Interpolation order = 4
>
> LOADING THE CONSTRAINED ATOMS AS GROUPS
>
>
> 5. REFERENCE ATOM COORDINATES
>
> default_name
>
> ----- READING GROUP 1; TITLE:
> RESTRAIN ALL
>
>
> GROUP 1 HAS HARMONIC CONSTRAINTS 1.00000
> GRP 1 RES 1 TO 9999
> Number of atoms in this group = 60028
> ----- END OF GROUP READ -----
> | EXTRA_PTS, trim_bonds: num bonds BEFORE trim =494860 0
> | EXTRA_PTS, trim_bonds: num bonds AFTER trim =494860 0
> | EXTRA_PTS, trim_bonds: num bonds BEFORE trim =175551 0
> | EXTRA_PTS, trim_bonds: num bonds AFTER trim = 14430 0
> | EXTRA_PTS, trim_theta: num angle BEFORE trim = 26427 0
> | EXTRA_PTS, trim_theta: num angle AFTER trim = 26427 0
> | EXTRA_PTS, trim_theta: num angle BEFORE trim = 20681 0
> | EXTRA_PTS, trim_theta: num angle AFTER trim = 20681 0
> | EXTRA_PTS, trim_phi: num diheds BEFORE trim = 52213 0
> | EXTRA_PTS, trim_phi: num diheds AFTER trim = 52213 0
> | EXTRA_PTS, trim_phi: num diheds BEFORE trim = 44220 0
> | EXTRA_PTS, trim_phi: num diheds AFTER trim = 44220 0
>
> --------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
> --------------------------------------------------------------------------------
>
> default_name
>
> begin time read from input coords = 0.000 ps
>
>
> Number of triangulated 3-point waters found: 161121
>
> Sum of charges from parm topology file = ************
> Assuming uniform neutralizing plasma
>
> | Dynamic Memory, Types Used:
> | Reals 20530835
> | Integers 36831804
>
> | Nonbonded Pairs Initial Allocation: 152666064
>
> | GPU memory information (estimate):
> | KB of GPU memory in use: 0
> | KB of CPU memory in use: 0
>
> --------------------------------------------------------------------------------
> 4. RESULTS
> --------------------------------------------------------------------------------
>
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
> 0.0
> Etot = -1339961.0208 EKtot = 0.0000 EPtot =
> -1339961.0208
> BOND = 678099.2680 ANGLE = 6687.3231 DIHED =
> 16633.1883
> 1-4 NB = 7536.6783 1-4 EEL = 6069.8294 VDWAALS =
> 377099.3948
> EELEC = -2438848.1051 EHBOND = 0.0000 RESTRAINT =
> 6761.4023
> EAMBER (non-restraint) = -1346722.4232
> ------------------------------------------------------------------------------
>
>
>
> ========================================
>
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Received on Wed Aug 14 2019 - 14:30:02 PDT
