Dear Amber users/developers,
I have a concern about visualizing amber trajectory (CPT with periodic
boundary conditions) using VMD, because the water molecules that went out of
the primary box did not have its image show up at the other side of the
primary box, which was what I used to see in the CHARMM CPT periodic box
simulations. I wonder if this is just designed this way, or is it because my
simulation code was not correct? Thank you! I used the simulation code as
below:
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,scee = 1.0,scnb = 1.0,
ig = 712,
cut = 8, ntr = 0,
ntc = 2, ntf = 2,
tempi = 323.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 100000, dt = 0.002,
ntpr = 10000, ntwx = 1000, ntwr = 1000
/
&ewald vdwmeth=0 /
/
END
eof
Best,
Mo Chen
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Received on Tue Jul 05 2011 - 11:30:03 PDT
