Dear All
At first I sent a comment about analysis the data of simulation and until
now nobody helped me. Could anybody help me specially computing the
solution's conductivity for ionic liquid solution in multi-run
simulations? the topic link is :
http://archive.ambermd.org/201402/0006.html
Also I simulate two sort of neutral molecules. I minimize the system but in
the simulation part an error was appeared.
I have two question?
1) what is ' ... RESTARTED DUE TO LINMIN FAILURE ...' ?
2) what is 'Error: Bad topology file. Sum of ATOMS_PER_MOLECULE does not
equal NATOM.' ?
Your sincerely
S. Nasiri
================ minimization =======================
mdin
minimization
&cntrl
imin=1, ntpr=10000, ntwx=10000, maxcyc=1000000,
ntb=1,
&end
/mpirun -np 24 -machinefile $PBS_NODEFILE sander.MPI -O -i mdin -o min.o -p
ionicbox.prmtop -c ionicbox.inpcrd -r min.x -x min.nc -e min.dat
cat min.o
NSTEP ENERGY RMS GMAX NAME NUMBER
1 1.1148E+07 2.1161E+06 7.5929E+07 H3 417
BOND = 4569.3824 ANGLE = 730.2598 DIHED =
644.1339
VDWAALS = 11141053.2883 EEL = 400.8070 HBOND =
0.0000
1-4 VDW = 58.4086 1-4 EEL = 831.0473 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
10000 -1.6611E+03 2.6740E-02 4.1399E-01 H3 1575
BOND = 72.7001 ANGLE = 244.5964 DIHED =
106.5248
VDWAALS = -1021.7606 EEL = -1926.8775 HBOND =
0.0000
1-4 VDW = 19.8753 1-4 EEL = 843.8442 RESTRAINT =
0.0000
... RESTARTED DUE TO LINMIN FAILURE ...
NSTEP ENERGY RMS GMAX NAME NUMBER
20000 -1.7098E+03 9.3918E-01 2.1960E+01 C4 2131
BOND = 75.2485 ANGLE = 245.8364 DIHED =
103.8039
VDWAALS = -1031.3753 EEL = -1966.1813 HBOND =
0.0000
1-4 VDW = 19.3287 1-4 EEL = 843.5733 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
30000 -1.7476E+03 1.4031E-02 2.4059E-01 C4 1845
BOND = 75.6741 ANGLE = 245.7849 DIHED =
104.9414
VDWAALS = -1046.3932 EEL = -1990.8059 HBOND =
0.0000
1-4 VDW = 19.4485 1-4 EEL = 843.7862 RESTRAINT =
0.0000
... RESTARTED DUE TO LINMIN FAILURE ...
NSTEP ENERGY RMS GMAX NAME NUMBER
40000 -1.7601E+03 4.9135E-03 1.6391E-01 O5 521
BOND = 75.2483 ANGLE = 246.8174 DIHED =
104.2039
VDWAALS = -1058.5034 EEL = -1990.9722 HBOND =
0.0000
1-4 VDW = 19.1185 1-4 EEL = 843.9431 RESTRAINT =
0.0000
... RESTARTED DUE TO LINMIN FAILURE ...
... RESTARTED DUE TO LINMIN FAILURE ...
... RESTARTED DUE TO LINMIN FAILURE ...
***** REPEATED LINMIN FAILURE *****
***** SEE
http://ambermd.org/Questions/linmin.html FOR MORE INFO *****
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
46223 -1.7620E+03 1.9896E-03 3.5060E-02 H2 518
BOND = 75.2691 ANGLE = 246.5636 DIHED =
104.0546
VDWAALS = -1058.6137 EEL = -1992.3980 HBOND =
0.0000
1-4 VDW = 19.1608 1-4 EEL = 843.9460 RESTRAINT =
0.0000
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Build the list 35.28 (91.79% of List )
| Other 3.15 ( 8.21% of List )
| List time 38.44 ( 0.10% of Nonbo)
| Short_ene time 83.87 (91.36% of Direc)
| Other 7.93 ( 8.64% of Direc)
| Direct Ewald time 91.81 ( 0.24% of Ewald)
| Fill Bspline coeffs 5.85 ( 0.02% of Recip)
| Fill charge grid 4.93 ( 0.01% of Recip)
| Scalar sum 4.00 ( 0.01% of Recip)
| Grad sum 10.22 ( 0.03% of Recip)
| FFT back comm time 23246.05 (76.29% of FFT t)
| Other 7226.47 (23.71% of FFT t)
| FFT time 30472.52 (91.99% of Recip)
| Other 2628.56 ( 7.94% of Recip)
| Recip Ewald time 33126.09 (86.66% of Ewald)
| Force Adjust 2845.84 ( 7.44% of Ewald)
| Virial junk 2160.76 ( 5.65% of Ewald)
| Ewald time 38226.86 (99.90% of Nonbo)
| Nonbond force 38265.38 (81.98% of Force)
| Bond/Angle/Dihedral 3.18 ( 0.01% of Force)
| FRC Collect time 4038.67 ( 8.65% of Force)
| Other 4367.96 ( 9.36% of Force)
| Force time 46675.17 (100.0% of Runmd)
| Runmd Time 46675.17 (99.83% of Total)
| Other 77.68 ( 0.17% of Total)
| Total time 46752.86 (100.0% of ALL )
| Highest rstack allocated: 20918
| Highest istack allocated: 501
| Final Performance Info:
| -----------------------------------------------------
| Average timings for all steps:
| Elapsed(s) = 46682.50 Per Step(ms) = **********
| ns/day = 0.00 seconds/ns = **********
| -----------------------------------------------------
| Job began at 17:29:13.886 on 02/18/2014
| Setup done at 17:30:24.534 on 02/18/2014
| Run done at 06:28:27.032 on 02/19/2014
| wallclock() was called 2034407 times
===================== simulation =======================
mdin.in
&cntrl
imin=0, ntpr=20000, ntwx=20000,
ntx=1, irest=0,
tempi=298., temp0=298., ntt=3, cut=10,
gamma_ln=5., ntb=2, ntp=1, taup=1.0, ioutfm=1, nstlim=2000000,
dt=.001, ig=-1,
&end
tail -200 md1.out
-------------------------------------------------------
Amber 12 SANDER 2012
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 12
| Run on 02/19/2014 at 08:12:27
[-O]verwriting output
File Assignments:
| MDIN: mdin.in
| MDOUT:
md1.out
| INPCRD:
min.x
| PARM:
ionicbox.prmtop
| RESTRT:
md1.x
| REFC:
refc
| MDVEL:
mdvel
| MDEN:
md1.dat
| MDCRD: md1.nc
| MDINFO:
mdinfo
|LOGFILE:
logfile
Here is the input file:
&cntrl
imin=0, ntpr=20000,
ntwx=20000,
ntx=1,
irest=0,
tempi=298., temp0=298., ntt=3,
cut=10,
gamma_ln=5., ntb=2, ntp=1, taup=1.0, ioutfm=1,
nstlim=2000000,
dt=.001,
ig=-1,
&end
Note: ig = -1. Setting random seed based on wallclock time in microseconds
and disabling the synchronization of random numbers between tasks
to improve performance.
| Conditional Compilation Defines Used:
| DIRFRC_COMTRANS
| DIRFRC_EFS
| DIRFRC_NOVEC
| MPI
| PUBFFT
| FFTLOADBAL_2PROC
| BINTRAJ
| Largest sphere to fit in unit cell has radius = 14.999
| New format PARM file being parsed.
| Version = 1.000 Date = 02/18/14 Time = 11:48:34
| 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 new box info from bottom of inpcrd
NATOM = 2258 NTYPES = 10 NBONH = 1454 MBONA = 501
NTHETH = 2693 MTHETA = 264 NPHIH = 1899 MPHIA = 330
NHPARM = 0 NPARM = 0 NNB = 7356 NRES = 303
NBONA = 501 NTHETA = 264 NPHIA = 330 NUMBND = 13
NUMANG = 23 NPTRA = 12 NATYP = 11 NPHB = 0
IFBOX = 1 NMXRS = 26 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Error: Bad topology file. Sum of ATOMS_PER_MOLECULE does not equal NATOM.
==============================================================
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Received on Wed Feb 19 2014 - 06:30:03 PST
