Dear amber users,
I am trying to equilibrate the total volume of the water box for 20 ps, at constant pressure (1atm) and
constant temperature (300K), and with positional restraints for CA and the crystal waters.
the input file:
&cntrl
imin = 0, irest = 0, ntx = 1,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 9, ntr = 1,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 25000, dt = 0.002,
ntpr = 50, ntwx = 50, ntwr = 50
restraintmask=':1-300.CA&:4799-40288', restraint_wt=10
/
I am getting such a error:
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 0 68 4641 4639
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
Could somebody help me to track the problem?
Urszula
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Received on Wed Oct 22 2008 - 05:09:52 PDT
