Dear all,
I would like to run an equilibrated structure (generated by another MD
program) consisting of 100 DME molecules with periodic boundary conditions. I
created a pdb file of the wrapped structure and created the .inpcrd file with
xleap. An in vacuo simulation of a single DME molecule works well, pbc
simulations from the tutorials as well. For some reasons AMBER gives a
segmentation fault. Is it crashing because the molecules are not put together?
Thanks in advance,
Diddo
Here's the output:
Here is the input file:
100 DME molecules
&cntrl
imin=0, irest=0, ntx=1,
ntt=2, temp0=298.0,
ntp=0, pres0=1.0,
ntb=1, ntc=2, ntf=2,
nstlim=10, dt=0.001,
ntwe=1, ntwx=1, ntpr=1,
cut=9.0,
/
&ewald
frameon=1, chngmask=1,
ew_type=0,
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
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 = 13.010
| New format PARM file being parsed.
| Version = 1.000 Date = 11/07/08 Time = 09:38:08
NATOM = 1800 NTYPES = 5 NBONH = 1000 MBONA = 700
NTHETH = 2200 MTHETA = 400 NPHIH = 1800 MPHIA = 800
NHPARM = 0 NPARM = 0 NNB = 8200 NRES = 100
NBONA = 700 NTHETA = 400 NPHIA = 800 NUMBND = 6
NUMANG = 7 NPTRA = 7 NATYP = 5 NPHB = 0
IFBOX = 0 NMXRS = 18 IFCAP = 0 NEXTRA = 200
NCOPY = 0
| Memory Use Allocated
| Real 170982
| Hollerith 10902
| Integer 132929
| Max Pairs 958320
| nblistReal 21600
| nblist Int 94236
| Total 6177 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 1, ntrx = 1, ntwr =
500
iwrap = 0, ntwx = 1, ntwv = 0, ntwe =
1
ioutfm = 0, 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
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 10, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00100, vlimit = 20.00000
Anderson (strong collision) temperature regulation:
ig = 71277, vrand = 1000
temp0 = 298.00000, tempi = 0.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
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 = 26.020 Box Y = 26.020 Box Z = 26.020
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 30 NFFT2 = 27 NFFT3 = 27
Cutoff= 9.000 Tol =0.100E-04
Ewald Coefficient = 0.30768
Interpolation order = 4
| EXTRA_PTS, trim_bonds: num bonds BEFORE trim = 1000 0
| EXTRA_PTS, trim_bonds: num bonds AFTER trim = 1000 0
| EXTRA_PTS, trim_bonds: num bonds BEFORE trim = 700 0
| EXTRA_PTS, trim_bonds: num bonds AFTER trim = 500 0
| EXTRA_PTS, trim_theta: num angle BEFORE trim = 2200 0
| EXTRA_PTS, trim_theta: num angle AFTER trim = 2200 0
| EXTRA_PTS, trim_theta: num angle BEFORE trim = 400 0
| EXTRA_PTS, trim_theta: num angle AFTER trim = 400 0
| EXTRA_PTS, trim_phi: num diheds BEFORE trim = 1800 0
| EXTRA_PTS, trim_phi: num diheds AFTER trim = 1800 0
| EXTRA_PTS, trim_phi: num diheds BEFORE trim = 800 0
| EXTRA_PTS, trim_phi: num diheds AFTER trim = 800 0
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 0
Sum of charges from parm topology file = -0.00000000
Forcing neutrality...
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
| # of SOLUTE degrees of freedom (RNDFP): 4400.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 4397. NUM_NOSHAKE = 0 CORRECTED RNDFP = 4397.
| TOTAL # of degrees of freedom (RNDF) = 4397.
---------------------------------------------------
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 = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 503358
| TOTAL SIZE OF NONBOND LIST = 503358
and here it crashes...
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Received on Fri Dec 05 2008 - 14:44:50 PST
