On 4/3/13 9:46 PM, Abhinav Agrawal wrote:
Hi,
I have a polymer box on which I wish to apply energy minimization.
However,
when I do energy minimization runs to polymer chain unravels and goes out
of the box. I guess this is because periodic conditions are not applied.
My em.mdp file is:
;
cpp = /usr/bin/cpp
define = -DFLEX_SPC
constraints = none
integrator = steep
nsteps = 1000
; Energy minimizing stuff
;
emtol = 2000
emstep = 0.01
nstcomm = 1
ns_type = grid
rlist = 1
rcoulomb = 1
rvdw = 1
Tcoupl = no
Pcoupl = no
gen_vel = no
pbc = xyz
This last line means PBC are being applied. Your observations are
consistent with using a box that is too small for the solute, but since you
haven't supplied information as to (1) what the system is, (2) how you
built it, or (3) how large the box is, there's very little to say beyond
speculation.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
I am using a composite system of polymer and clay. The composite box (5.8
nm * 5.8 nm *7 nm) is made from combining a polymer box (5.7 nm * 5.7 nm *
5.7 nm) and clay box (5.5 nm * 5.1 nm * 1 nm) using editconf and genbox.
Should I increase the size of the composite box. Also, If I increase the
size of the box how do I ensure that the density of the system does not
chance. Thanks for your help.
No, the box size seems reasonable. I only suggested that because the behavior
you described (unfolding of the polymer) seemed to indicate spurious forces
across PBC. As Tsjerk rightly noted, there's no such thing as "outside" of an
infinite system.
Without the exact sequence of commands and links to before and after images of
the behavior you're seeing, there's not really much anyone can do to help.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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