[gmx-users] A question for em before the INM analysis

[Tanping Li]

Dear all,

I am trying to do the INM analysis for a small system:
one residue Trp in water. Before I do the g_nmeig, I
need to minimize the whole structure use em. Should I
minimize tbe whole system, or ONLY the protein
conformation in vacuum, as I see some people did in
mailing list? Since I find it is realy hard to
minimize the whole system to the level Fmax=0.01. I
use the flexible SPCE water and following is the em.mp
I am using:


cpp                 =  /lib/cpp
constraints         =  none
integrator          =  l-bfgs
nsteps              =  50000
;
;	Energy minimizing stuff
;
emtol               =  0.000000001
emstep              =  0.000001
nstcgsteep          =  1000

pbc                 =  no 
nstlist             =  0 
nstcomm             =  1
ns_type             =  simple
rlist               =  0
rcoulomb            =  0
rvdw                =  0
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no



Is there problem in my mdp file? Really appretiate
your suggestion and help.


Best
Tanping