[gmx-users] Re: protein unfolding

[Aina Quintilla]

> >hi,
> >
> >i am looking at the behaviour of a protein 1l2y.
> >during the run the protein is unfolding.. at every temperature, from 200 K
> > ...
> >
> >i am using the gromos96 43a1 force field
> >
> >could anyone give me a hint about what is happening? is gromacs force
> > field not adequate to work with it?
> >
> >i attach the input file (.pdb) of the run
>
> You might want to give some information about the way you simulate the
> protein.
> What protocol did you follow ?
> XAvier
>
> --

i did an energy minimization of the solved protein, then a short run 
restraining the positions of the protein, and then a mdrun whose parameters 
are:

constraints         =  all-bonds
integrator          =  md
dt                  =  0.002	; ps !
nsteps              =  5000000	
nstcomm             =  1
nstxout             =  5000
nstvout             =  0
nstfout             =  0
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tau_t               =  0.1	     0.1
tc-grps		    =  protein	     sol
ref_t               =  300	     300
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529

shoud i use PME for coulomb interactions?

thank you