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'
/
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Received on Wed Aug 17 2011 - 19:30:03 PDT
