On Mon, 26 Nov 2007 13:45:01 +0530 (IST)
[EMAIL PROTECTED] wrote:
Hi All,
I have been trying run energy minimization for a homoTRIMER protein, I
have puzzled by the following results!
1) energy minimization in vacuum 1 chain is separated from the remaining 2
chains. I tried for 5 models in 4 models chains are separated and one is
normal.
2)energy minimization in box with or with out solvent, no chain separation
for all the 5 models.
please note that EM method is steepest decent, I have tried size on the
box up to 20nm.
you are probably experiencing the effect of PBC. In the cases you
see "separation", centering the protein in the box should solve the
problem.
CONTESTS OF MDP FILE
cpp = /usr/bin/cpp
define = -DFLEX_SPC
constraints = none
integrator = steep
nsteps = 100
;
; Energy minimizing stuff
;
emtol = 2000
emstep = 0.01
nstcomm = 1
ns_type = grid
rlist = 1
rcoulomb = 1.0
rvdw = 1.0
Tcoupl = no
Pcoupl = no
gen_vel = no
What would be the probable reason for this. Please let me know.
Regards
Chandu
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-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
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