[gmx-users] Chains blowing Apart

csreddy at ncbs.res.in csreddy at ncbs.res.in
Mon Nov 26 09:15:01 CET 2007

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
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.


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.


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