Hi people,
I have a such strange problem that I don't even know how to start
explaining. I'm simulating a DNA in a truncated octahedron box. Then, I run
a series of simulations on it, but when I switch iwrap=1,
the coordinates written on the output don't match the positions of the
atoms, I don't see funny lines, but the entire system is shifted and it
seems that the origin is not on the center of the box (you realize it when
you try to rotate the system on VMD, it rotates around a center which is not
inside the cell).
Also the DNA is not at the center of the box anymore, it goes close to the
border. However, when I turn off iwrap, everything goes fine, the output
coordinates (always read "AMBER coordinates with periodic box" on VMD,
otherwise I DO get funny lines) keep the cell at the right place and the DNA
is, as expected, at the center of the box. Here is my md9.in file:
Unrestrained MD
&cntrl
irest=1, ntx=7,
ntf=2, ntb=2, cut=9.0,
nstlim=1000, dt=0.002,
temp0=300.0, ntt=1, *iwrap=1,
* ntp=1,
ntc=2,
ntwx=50,
/
and the command used to run it:
l=md8
f=md9
$sander -i $f.in -o $f.out -inf $f.inf \
-c 1D20_wat_tip4pew.$l -ref 1D20_wat_tip4pew.$l -r
1D20_wat_tip4pew.$f \
-p 1D20_wat_tip4pew.top -x 1D20_wat_tip4pew$f.x -e
1D20_wat_tip4pew$f.ene
I also tested 2 followed simulations with and without iwrap, and I realized
that when I turn it on, the system is shifted from the center and the DNA is
no longer at the center of the new box position. Any idea? Do I REALLY need
iwrap for long simulations?
--
--
Bruno Barbosa Rodrigues
PhD Student - Physics Department
Universidade Federal de Minas Gerais - UFMG
Belo Horizonte - Brazil
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Received on Thu Jul 28 2011 - 14:30:04 PDT
