[gmx-users] Minimizing an average structure

[Andrea Carotti]

Hi all,
    i've obtained an average structure from my trajectory (2 chains: 
36+259aa), and now i'm trying to minimize it in vacuum . I' ve tried with an 
SD followed by a CG protocol taken from page 15 of this tutorial 
http://www2.umdnj.edu/~kerrigje/pdf_files/fwspidr_tutor.pdf.
SD in vacuo
; User kerrigan (236)
;
; Input file
;
cpp = /usr/bin/cpp
constraints = none
integrator = steep
nsteps = 400
;
; Energy minimizing stuff
;
emtol = 1000
emstep = 0.01
nstcomm = 1
ns_type = grid
morse = no
coulombtype = Shift
vdw_type = Shift
rlist = 1.0
rcoulomb = 1.2
rvdw = 1.2
rcoulomb_switch = 1.0
rvdw_switch = 1.0
epsilon_r = 6.0
Tcoupl = no
Pcoupl = no
gen_vel = no

CG
; in vacuo
; User kerrigan (236)
;
; Input file
;
cpp = /usr/bin/cpp
constraints = none
integrator = cg
nsteps = 3000
;
; Energy minimizing stuff
;
emtol = 100
emstep = 0.01
nstcgsteep = 1000
nstcomm = 1
morse = yes
coulombtype = Shift
vdw_type = Shift
ns_type = grid
rlist = 1.0
rcoulomb = 1.2
rvdw = 1.2
rcoulomb_switch = 1.0
rvdw_switch = 1.0
epsilon_r = 6.0
Tcoupl = no
Pcoupl = no
gen_vel = no

Now appears my problem:  the light chain goes away from the heavy chain and 
lost all the interactions with it. There is a setting to prevent this 
repulsion? I'm doing something wrong?
I will be happy also to know some other experiences and protocols about this 
kind of minimization.
Thanks
Andrea



------------
Andrea Carotti
Dip. Farmaco-chimico (Università di Bari)
via E. Orabona, 4 ## CAP 70124 ## BARI (Italy)
web: http://www.farmchim.uniba.it/samba/
phone: (+39) 080 5442551  ##   fax: (+39) 080 5442230