[gmx-users] Pushing MD further

[Thielges, Sabine]

Hi,

I am currently running some GPRC MD with membrane. After a lot of trial
I now have a nice 25 ns run with an agonist. But the final structure is
too close the starting and I know it is far from what the biology
describes. 
I would like to know if there is options that I can add to my md.mdp
file to make the MD "explores some other area". 

Md.mdp:

title		= Production MD 
; Run parameters
integrator	= md		; leap-frog integrator
nsteps		= 10000000	; (20 ns)
dt		= 0.002		; 2 fs
; Output control
nstxout		= 1000		; save coordinates every 2 ps
nstvout		= 1000		; save velocities every 2 ps
nstxtcout	= 1000		; xtc compressed trajectory output every
2 ps
nstenergy	= 1000		; save energies every 2 ps
nstlog		= 1000		; update log file every 2 ps
; Bond parameters
continuation	= yes		; Restarting after NPT 
constraint_algorithm = lincs	; holonomic constraints 
constraints	= all-bonds	; all bonds (even heavy atom-H bonds)
constrained
lincs_iter	= 1		; accuracy of LINCS
lincs_order	= 4		; also related to accuracy
; Neighborsearching
ns_type		= grid		; search neighboring grid cels
nstlist		= 5		; 10 fs
rlist		= 1.2		; short-range neighborlist cutoff (in
nm)
rcoulomb	= 1.2		; short-range electrostatic cutoff (in
nm)
rvdw		= 1.2		; short-range van der Waals cutoff (in
nm)
; Electrostatics
coulombtype	= PME		; Particle Mesh Ewald for long-range
electrostatics
pme_order	= 4		; cubic interpolation
fourierspacing	= 0.16		; grid spacing for FFT
; Temperature coupling is on
tcoupl		= Nose-Hoover		; More accurate thermostat
tc-grps		= Protein DRG POP SOL_CL-	; three coupling groups
- more accurate
tau_t		= 0.1	0.1	0.1  0.1	; time constant, in ps
ref_t		= 310 	310	310 310	; reference temperature, one for
each group, in K
; Pressure coupling is on
pcoupl		= Parrinello-Rahman	; Pressure coupling on in NPT
pcoupltype	= semiisotropic		; uniform scaling of x-y box
vectors, independent z
tau_p		= 2.0			; time constant, in ps
ref_p		= 1.0	1.0		; reference pressure, x-y, z (in
bar)
compressibility = 4.5e-5	4.5e-5	; isothermal compressibility,
bar^-1
; Periodic boundary conditions
pbc		= xyz		; 3-D PBC
; Dispersion correction
DispCorr	= EnerPres	; account for cut-off vdW scheme
; Velocity generation
gen_vel		= no		; Velocity generation is off 
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm		= 1
comm-mode	= Linear
comm-grps	= Protein_DRG_POP SOL_CL


Thank you in advance

Sabine