Hi All,
During the heating up of system using following script, the shape of water
box is badly disturbed. I am using TIP3P was water type and cubic water
box. Even after the heating step, the protein is well inside the waterbox
only the shape of waterbox is badly disturbed.
Heating up the system equilibration stage 1
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 10.0,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nrespa=2,
nstlim = 100000, dt = 0.002,
ntpr = 100, ntwx = 100, ntwr = 1000,
/
Keep Protein fixed with weak restraints
10.0
RES 1 122
END
END
My question is "shall I continue to the next step with the same system or
shall I re-frame the waterbox around the protein?"
Hirdesh
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Received on Sun Sep 05 2010 - 23:30:03 PDT
