Dear Amber ,
I tried Targeted Molecular Dynamics
by giving the mask to all the atoms
and i gave all the atom flags in the input
the total number of atoms are 1296
but when i run the script it shows
only 1062 atoms matches
my input file is as follows
&cntrl
imin = 0,
irest = 0 ,
ntb = 0,
ntxo = 1,
ntx =1,
tempi =300.0
ntb = 0,
ntc=2,
ntr =0,
ntf = 2,
igb = 1,
nscm = 100,
ntwr = 1000
ntpr = 100,
ntwx = 100,
ntwv =100,
ntwe = 100,
ntt = 3,
gamma_ln = 1.0,
temp0 = 300.0
nstlim = 10000,
dt = 0.001,
cut = 999,
itgtmd=1,
tgtrmsd =0.5 ,
tgtmdfrc = 10.0,
tgtfitmask= ":1-40 . P,O1P,O2P,O5',C5',C4',O4',C1',C6,C5,C2,O2,C4,C3',C2',O3',H5T,1H5',2H5',H4',H1',N1,C6,H6,H5,N4,1H4,2H4,N3,H3',1H2',2H2',N9,C8,H8,N7,O6,H1,N2,1H2,2H2,C7,1H7,2H7,3H7,O4,H3,N6,1H6,2H6,H2,H3T,Na+",
tgtrmsmask= ":1-40 . P,O1P,O2P,O5',C5',C4',O4',C1',C6,C5,C2,O2,C4,C3',C2',O3',H5T,1H5',2H5',H4',H1',N1,C6,H6,H5,N4,1H4,2H4,N3,H3',1H2',2H2',N9,C8,H8,N7, O6,H1,N2,1H2,2H2,C7,1H7,2H7,3H7,O4,H3,N6,1H6,2H6,H2,H3T,Na+",
/
and the run got stopped with the error
--------------------------------------------
vlimit exceeded for step 34; vmax = 20.9476
Coordinate resetting (SHAKE) was not accomplished
within 3000 iterations
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
----------------------------------------------------------------------
Is there any problem in the mask atom flags !
what does this error mean !
thanks in advance
balaji
UOM
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Received on Wed Feb 25 2009 - 08:24:16 PST
