Read the manual, in particular the section about the iwrap keyword.
By the way, unless you have a VERY particular reason to do so, ALWAYS
set the ig value to -1
Also read the manual about why this must be so.
Adrian
On 7/5/11 8:08 PM, Mo Chen wrote:
> 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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>
--
Dr. Adrian E. Roitberg
Full Professor
Quantum Theory Project, Department of Chemistry
University of Florida
on Sabbatical in Barcelona until August 2011.
Email roitberg.ufl.edu
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Received on Tue Jul 05 2011 - 11:30:04 PDT
