Dear all,
I am running an md simulation using Amber9. After energy minimization
and restrained dynamics (increasing the system temperature from Ok to
300K), I performed equilibration for 200ps and I found all the
aromatic rings (in Phe, Tyr, His, etc) have lost their planarity. That
sounds unreasonable but I cannot figure out what's wrong with my input
file. I used leaprc.ff99 and my md input file follows,
&cntrl
imin = 0,
ntx = 7, irest = 1,
ntb = 2, pres0 =1.0, ntp = 1,
taup = 2,
ntr = 0,
cut = 10,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 100000, dt = 0.002,
ntpr = 100, ntwx = 500, ntwr = 1000
/
END
Thanks in advance to anyone that will give any suggestion.
Amara
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Received on Wed Apr 23 2008 - 06:07:34 PDT
