Hi,
When using pmemd.MPI, I get
Coordinate resetting cannot be accomplished,
deviation is too large
iter_cnt, my_bond_idx, i and j are : 1 1 86 119
whereas serial pmemd works just fine...
Here's my heating.mdin
&cntrl
imin = 0, !no mininisation
irest = 0, !no trajectory restart
ntx = 1, !only coordinates are read in
dt = 0.002, !2fs time step
ntc = 2, !SHAKE; bonds involving H are constrainted
ntf = 2, !all H-atom bonds forces are not evaluated
nsnb = 25,
tol = 0.000001, !Shake tolerance 10 times tighter
ntb = 0, !no periodicity and PME off!
ntp = 0, !No pressure control
cut = 9999.0, !9999A cut off
igb = 2,
rgbmax = 9999.0, !default max dist between atom pairs Born radii calc.
saltcon= 0.2, !salt concentration (M)
ntt = 3, !constant temp using langevin
tempi = 0.0, !initial temp = 0K
temp0 = 300.0, !final temp = 300K
gamma_ln = 1.0, !1.0 per ps for collision freq
ntpr = 500, !print details to log every 500 steps
ntwx = 500, !write coordinates to mdcrd every 500 steps
ntwr = 50000, !write restart file to heat.rst every 50000 steps
iwrap = 0, !wrap periodic molecules.
nstlim = 850000, !run for 850,000 steps
ntr = 1, !restraints
restraint_wt=2.0, ! Weight
restraintmask=".CA,C,O,N", !Backbone atoms selection
nscm = 0, !No removal of COM motion
nmropt = 1, !Scale temp target.
ig = -1, !Random seed based on wallclock.
ioutfm = 1, !NetCDF MDCRD.
/
&wt type='TEMP0', istep1=0,istep2=600000,
value1=0.0, value2=300.0
/
&wt type='TEMP0', istep1=600001,istep2=850000,
value1=300.0, value2=300.0
/
&wt type='END'
/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 17 2011 - 19:30:03 PDT
