Friends,
I am submitting a job, using the following control list, i am using
pmemd.cuda.MPI in amber12 version.
&cntrl
IMIN = 0, NTPR = 2000, NTWR = 1000 , NTWX = 2000 , IREST = 1 , NTX =
5,
NTXO = 2, IOUTFM =1 , iwrap = 1 ,
CUT = 12.0 ,
NSTLIM = 15000000 , dt = 0.002 ,
ntt = 3 , tempi = 303.0 , temp0 = 303.0 , gamma_ln = 2.0 , ig = -1,
ntp = 1 , ntc = 2 , ntf = 2 , ntb = 2 , nsnb = 100 ,
/
The simulations doest start, the output shows information till:
"Intermolecular bonds treatment". Since no error indicated, i am not
getting what could be the problem. I visualized the rstart file of previous
run and i see no abnormalities. Am i making some mess in the "cntrl" list ?.
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
getting new box info from bottom of inpcrd
NATOM = 183503 NTYPES = 17 NBONH = 179399 MBONA = 4180
NTHETH = 9251 MTHETA = 5665 NPHIH = 18394 MPHIA = 14283
NHPARM = 0 NPARM = 0 NNB = 278947 NRES = 58975
NBONA = 4180 NTHETA = 5665 NPHIA = 14283 NUMBND = 42
NUMANG = 87 NPTRA = 43 NATYP = 29 NPHB = 1
IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 17 17 17
| Direct force subcell size = 7.2352 7.2462 7.2424
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 5, irest = 1, ntrx = 1
Nature and format of output:
ntxo = 2, ntpr = 2000, ntrx = 1, ntwr =
1000
iwrap = 1, ntwx = 2000, ntwv = 0, ntwe
= 0
ioutfm = 1, ntwprt = 0, idecomp = 0,
rbornstat= 0
Potential function:
ntf = 2, ntb = 2, igb = 0, nsnb
= 50
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 15000000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = -1.00000
Langevin dynamics temperature regulation:
ig = 247149
temp0 = 303.00000, tempi = 303.00000, gamma_ln= 2.00000
Pressure regulation:
ntp = 1
pres0 = 1.00000, comp = 44.60000, taup = 1.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
| Intermolecular bonds treatment:
C. Balasubramanian
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Received on Mon Sep 14 2015 - 01:00:03 PDT
