Hi, Amber users-
I'm basically following the steps on the "DNA"
tutorial
to do some MD on proteins. I couldn't get my dynamics
going because "vlimit exceeded" and "Coordinate
resetting (SHAKE) cannot be accomplished". Does anyone
know how to fix it?
Appreciate!
Here's my "md_ntr.in" file:
-------------------
&cntrl
nmropt = 0,
ntx = 1, irest = 0, ntrx = 1,
ntxo = 1,
ntpr = 100, ntwx = 500, ntwv = 0,
ntwe = 0,
ntf = 2, ntb = 2,
cut = 8.0, nsnb = 10,
ibelly = 0, ntr = 1,
imin = 0,
nstlim = 250,
nscm = 0,
t = 0.0, dt = 0.002,
temp0 = 263.15, tempi = 263.15,
ig = 71277, heat = 0.0,
ntt = 1,
tautp = 0.2,
vlimit = 15.0,
ntp = 1, pres0 = 1.0, comp = 44.6,
taup = 0.2, npscal = 1,
ntc = 2, tol = 0.00001
&end
Hold the protein fixed
500.0
RES 1 88
END
END
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Received on Wed Jan 14 2004 - 15:53:11 PST
