Hello,
I was under the impression that all I had to do to turn on SHAKE in a
pmemd dynamics run was set ntf = 2 and ntc = 2; however, when I do this I
find that bonds containing hydrogen are still fluctuating. This creates
problems, of course, when polar hydrogens come too near a negatively
charged atom and cause the simulation to crash.
Here is my input file. Can anyone suggest a remedy?
>>>>>
Round 1 of MD equilibration
&cntrl
nmropt = 0,
ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
ntpr = 100, ntwx = 1000, ntwv = 0, ntwe = 100,
iwrap = 1, ioutfm = 0,
ntf = 2, ntb = 1,
cut = 9.0,
ibelly = 1, ntr = 0,
imin = 0,
nstlim = 100000,
nscm = 1000,
t = 0.0, dt = 0.0005,
temp0 = 293.0, tempi = 0.0,
ig = 9376841,
ntt = 3,
gamma_ln = 3.0,
vlimit = 20.0,
ntp = 0, pres0 = 1.0, comp = 44.6,
taup = 1.0,
ntc = 2, tol = 0.001, watnam = 'WAT ',
&end
Group input for restraint mask
FIND
SEARCH
ATOM 1 29008
END
END
<<<<<
Thanks!
Dave
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Received on Sun Sep 16 2007 - 06:07:52 PDT
