Dear All,
I ran amber10/sander.MPI with PME + cutoff = 0 -> sander crashes
amber12/sander.MPI with PME + cutoff = 0 -> sander crashes
(compiled with intel13 + mkl)
amber12/pmemd.MPI with PME + cutoff = 0 -> pmemd does not crash...
Printed output: printing stops in section 4:
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
| # of SOLUTE degrees of freedom (RNDFP): 24936.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 24933. NUM_NOSHAKE = 0 CORRECTED RNDFP = 24933.
| TOTAL # of degrees of freedom (RNDF) = 24933.
-> nothing else is printed...
In Fox & Kollman J.Phys.Chem.B 1998, 102, 8070, MD simulation with
cutoff = 0 is reported & Sander from Amber 4.1 was used.
Why does sander crash, while pmemd does not crash in this case?
(with the same input & cut = 12, sander does not crash)
thank you, regards,
Francois
# Cst pressure simulation with cutoff = 0 Angs; 300 K short
$PARAL -np $NPROC $EXE -O -i md-cstpres0.in \
-o md-cstpres0b.out \
-p $mol.parm7 \
-c md-cstvol.rst7 \
-r md-cstpres0b.rst7 \
-x md-cstpres0b.mdcrd
my test input below:
cst pressure MD, nstlim*dt psec, PME with cutoff
&cntrl
nmropt = 0, ioutfm = 1, iwrap = 0,
ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
ntpr = 100, ntwr = 1000, ntwx = 500,
ntave = 0, ntwv = 0, ntwe = 0,
ntf = 2, ntb = 2,
ntc = 2, tol = 0.00001,
dielc = 1, ipol = 0,
cut = 0, ig = 71277, comp = 52.5,
ibelly = 0, ntr = 0, igb = 0,
imin = 0, nstlim = 5000,
nscm = 1000, t = 0.0, dt = 0.002,
temp0 = 300, tempi = 300,
ntt = 1, tautp = 0.2, vlimit = 20,
ntp = 1, pres0 = 1.0, taup = 0.2,
&end
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Received on Sun Feb 23 2014 - 09:30:03 PST
