Dear Amber users!
Recently I've performed test NPT simulation ( below you can see details of
setup) of my water soluble protein. During analysis of the production
trajectory I've noticed constant rigid-body-like diffusion of my protein
across boundaries of PB (molecule crossed box boundaries many time). How I
could avoid of this ? Does the iwrap = 1 flag influence on such behavior ?
02md.in: equilibration
&cntrl
imin = 0, ntx = 1, irest = 0, nstlim = 5000000,
temp0 = 310.00, tempi = 310.00, ig = 71287,
ntc = 2, ntf = 2, ntt = 1, dt = 0.002,
ntb = 2, ntp = 1, tautp = 1.0, taup = 1.0,
ntwx = 500, ntwe = 0, ntwr = 500, ntpr = 500,
cut = 10.0, iwrap = 1,
ntr = 1, nscm = 500,
/
END
James
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Received on Tue May 20 2014 - 02:30:02 PDT
