AMBER Archive (2008)

Subject: AMBER: Emperical Valence Bond

From: sai kumar ramadugu (amberquestions_at_gmail.com)
Date: Tue Sep 09 2008 - 16:46:25 CDT

Dear Prof Case,
   I'm running EVB molecular dynamics for two states of a dye molecule in
ionic liquid. The total number of atoms in the system is 9300.
When I ran the EVB MD with the same dye in Acetonitrile, the MD run was
successful. But with the ionic liquid, the run does not progress at all and
the output file stops at a particular point (no matter how long I wait). I'm
pasting the output file for one of the states.

*OUTPUT FILE*

          -------------------------------------------------------
          Amber 9 SANDER 2006
          -------------------------------------------------------
| Run on 09/09/2008 at 18:18:48
  [-O]verwriting output
File Assignments:
| MDIN: npt-st-2.in
| MDOUT: md-st-2-1.out
|INPCRD: new.rst7
| PARM: st-2-1.parm7
|RESTRT: md-npt-st-2-1.rst7
| REFC: new.rst7
| MDVEL: mdvel
| MDEN: mden-1
| MDCRD: md-npt-st-2-1.crd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip

 Here is the input file:
CVL molecular dynamics in Acetonitrile
 &cntrl
   ntwe = 1, ntwx = 10000, ntwv = 10000, ntpr = 1, ievb = 1,
   ntt = 1, temp0 = 300.0, tempi = 300.0, tautp = 0.01,
   igb = 0, nsnb = 1,
   scnb = 2.0, scee = 2.0, dielc = 1, cut = 9.0,
   ntb = 2, ntc = 1, ntf = 1,
   nstlim =1000000, dt = 0.0010,
   ntp = 1, taup = 0.1, comp = 44.6, pres0 = 1.0,
   ibelly = 0, ntr = 0,
   imin = 0, irest = 1, ntx = 5,
 &end
--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MPI
 getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 22.367
| New format PARM file being parsed.
| Version = 1.000 Date = 09/08/08 Time = 14:16:48
 NATOM = 9300 NTYPES = 12 NBONH = 3989 MBONA = 5094
 NTHETH = 9298 MTHETA = 8191 NPHIH = 15046 MPHIA = 9544
 NHPARM = 0 NPARM = 0 NNB = 49150 NRES = 441
 NBONA = 5094 NTHETA = 8191 NPHIA = 9544 NUMBND = 18
 NUMANG = 30 NPTRA = 20 NATYP = 16 NPHB = 0
 IFBOX = 1 NMXRS = 60 IFCAP = 0 NEXTRA = 0
 NCOPY = 0

| Memory Use Allocated
| Real 557773
| Hollerith 56243
| Integer 776191
| Max Pairs 2063050
| nblistReal 111600
| nblist Int 473811
| Total 18390 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

     BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
   2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------

General flags:
     imin = 0, nmropt = 0
Nature and format of input:
     ntx = 5, irest = 1, ntrx = 1
Nature and format of output:
     ntxo = 1, ntpr = 1, ntrx = 1, ntwr =
500
     iwrap = 0, ntwx = 10000, ntwv = 10000, ntwe
= 1
     ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0
Potential function:
     ntf = 1, ntb = 2, igb = 0, nsnb
= 1
     ipol = 0, gbsa = 0, iesp = 0
     dielc = 1.00000, cut = 9.00000, intdiel = 1.00000
     scnb = 2.00000, scee = 2.00000
Frozen or restrained atoms:
     ibelly = 0, ntr = 0
Molecular dynamics:
     nstlim = 1000000, nscm = 1000, nrespa = 1
     t = 0.00000, dt = 0.00100, vlimit = 20.00000
Berendsen (weak-coupling) temperature regulation:
     temp0 = 300.00000, tempi = 300.00000, tautp = 0.01000
Pressure regulation:
     ntp = 1
     pres0 = 1.00000, comp = 44.60000, taup = 0.10000
Ewald parameters:
     verbose = 0, ew_type = 0, nbflag = 1, use_pme
= 1
     vdwmeth = 1, eedmeth = 1, netfrc = 1
     Box X = 44.735 Box Y = 46.792 Box Z = 46.983
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 48 NFFT2 = 48 NFFT3 = 48
     Cutoff= 9.000 Tol =0.100E-04
     Ewald Coefficient = 0.30768
     Interpolation order = 4

*Reading EVB input file from input.st1*
*EVB options:
     nevb = 2, nbias = 0, nmorse = 0, ntw_evb = 1
     xch_type = constant
     evb_dyn = groundstate
     dia_shift( 1) = 0.00000
     dia_shift( 2) = 0.00000
     xch_cnst( 1, 2) = 1.00000*

---------------------------------------------------------------------------------------
After reading the EVB input file the program runs forever and does not
generate any output.
When I kill the job, I see the following in the error file.

*ERROR FILE*

forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
sander.MPI 000000000086482D Unknown Unknown Unknown
sander.MPI 0000000000864157 Unknown Unknown Unknown
sander.MPI 000000000086375D Unknown Unknown Unknown
sander.MPI 00000000008BEA63 Unknown Unknown Unknown
sander.MPI 0000000000425B22 Unknown Unknown Unknown
sander.MPI 0000000000414215 Unknown Unknown Unknown
sander.MPI 00000000004E1C8E Unknown Unknown Unknown
sander.MPI 00000000004B8E03 Unknown Unknown Unknown
sander.MPI 00000000004B34D7 Unknown Unknown Unknown
sander.MPI 000000000040566A Unknown Unknown Unknown
libc.so.6 0000003C7FE1D084 Unknown Unknown Unknown
sander.MPI 00000000004055A9 Unknown Unknown Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
sander.MPI 000000000086482D Unknown Unknown Unknown
sander.MPI 0000000000864157 Unknown Unknown Unknown
sander.MPI 000000000086375D Unknown Unknown Unknown
sander.MPI 00000000008BEA63 Unknown Unknown Unknown
sander.MPI 0000000000425B22 Unknown Unknown Unknown
sander.MPI 0000000000414215 Unknown Unknown Unknown
sander.MPI 00000000004E1C8E Unknown Unknown Unknown
sander.MPI 00000000004B8E03 Unknown Unknown Unknown
sander.MPI 00000000004B34D7 Unknown Unknown Unknown
sander.MPI 000000000040566A Unknown Unknown Unknown
libc.so.6 0000003C7FE1D084 Unknown Unknown Unknown
sander.MPI 00000000004055A9 Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
forrtl: error (78): process killed (SIGTERM)
forrtl: error (78): process killed (SIGTERM)
forrtl: error (78): process killed (SIGTERM)
forrtl: error (78): process killed (SIGTERM)
--------------------------------------------------------------------------------------

When I checked online about *forrtl: severe (174): SIGSEGV, segmentation
fault occurred *
it says about the memory issues.

Can I please get some help regarding this?

Thanks a ton!

Regards,
Sai 

-- 
Sai K. Ramadugu
The Margulis Lab,
Dept of Chemistry,
Univ of Iowa

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