Hi, all.
I plan to run my CpHMD job on 208 processors at 26 nodes, but it's stopped
with Error "Must have more residues than processors!"
Now I redo the job on 80 processors and no problem.
Could anyone explain the reason of the error?
Weather the number of processors cannot more than the numbers of system's
residues?
A part of mdout:(I also attach the mdout and log file to make more
information)
-------------------------------------------------------
Amber 12 SANDER 2012
-------------------------------------------------------
| Run on 10/02/2013 at 00:16:02
[-O]verwriting output
File Assignments:
| MDIN: heat.mdin
| MDOUT: 1ag2.heat.mdout
|INPCRD: 1ag2.min.rst7
| PARM: 1ag2.parm7
|RESTRT: 1ag2.heat.rst7
| REFC: 1ag2.min.rst7
| MDVEL: mdvel
| MDEN: mden
| MDCRD: 1ag2.heat.mdcrd
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
|
Here is the input file:
Implicit solvent constant pH initial heating mdin
&cntrl
imin=0, irest=0, ntx=1,
ntpr=500, ntwx=500, nstlim=1000000,
dt=0.002, ntt=3, tempi=10,
temp0=300, tautp=2.0, ig=-1,
ntp=0, ntc=2, ntf=2, cut=30,
ntb=0, igb=2, tol=0.000001,
nrespa=1, saltcon=0.1, icnstph=1,
ntcnstph=100000000,
gamma_ln=5.0, ntwr=500, ioutfm=1,
nmropt=1, ntr=1, restraint_wt=2.0,
restraintmask='.CA,C,O,N',
/
&wt
TYPE='TEMP0', ISTEP1=1, ISTEP2=500000,
VALUE1=10.0, VALUE2=300.0,
/
&wt TYPE='END' /
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MPI
| New format PARM file being parsed.
| Version = 1.000 Date = 10/01/13 Time = 16:36:54
NATOM = 1717 NTYPES = 14 NBONH = 853 MBONA = 885
NTHETH = 1885 MTHETA = 1197 NPHIH = 3799 MPHIA = 2875
NHPARM = 0 NPARM = 0 NNB = 9346 NRES = 103
NBONA = 885 NTHETA = 1197 NPHIA = 2875 NUMBND = 44
NUMANG = 106 NPTRA = 41 NATYP = 26 NPHB = 0
IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are H(N)-modified Bondi radii (mbondi2)
| Memory Use Allocated
| Real 112087
| Hollerith 5256
| Integer 110696
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 1328 kbytes
| 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
Note: ig = -1. Setting random seed based on wallclock time in microseconds
and disabling the synchronization of random numbers between tasks
to improve performance.
......
......
5. REFERENCE ATOM COORDINATES
defa
Mask .CA,C,O,N; matches 412 atoms
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
defa
begin time read from input coords = 0.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
TEMP0 1 500000 10.000000 300.000000 0 0
RESTRAINTS:
** No restraint defined **
Done reading weight changes/NMR restraints
Number of triangulated 3-point waters found: 0
Must have more residues than processors!
Thanks a lot!
Jacky
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- application/octet-stream attachment: blog.7458
Received on Tue Oct 01 2013 - 09:30:04 PDT
