[gmx-users] problem with 53a6 simulating a coiled-coil fiber like protein

Lory Montout lory.montout at gmail.com
Mon Jul 20 13:50:08 CEST 2009

Dear all

I recently performed MD simulations using 53A6 force field with
Gromacs4.0 The system includes a protein+water and ions for
neutralizing, The protocol is quite classical: NPT ensemble, 300K and
reaction field for electrostatics, 2fs for integration, bond lengths are
The protein is a coiled-coil fiber like protein, including different  
repeat units. At the
starting point, the protein  roughly adopts a cylinder shape. After
few ns ( less than 5), some helices are broken,  even unfold. Finally,
the protein is kinked,with a kink angle  ~ 90°. I tested different
constructions but observed similar results.
The same system was simulated with NAMD, charmm force field, the
structure remains stable all along the simulation (10ns for now ).
Did anyone obtain similar results for a coiled coil  system with 53A6
force field?

here is my .mdp file :

nstvout             =  10000
nstfout             =  0
nstxtcout           =  2500
xtc_precision       =  1000
nstlog              =  500
nstenergy           =  500
nstlist             =  5
rlist               =  0.8
coulombtype         =  generalized-reaction-field
rcoulomb            =  1.4
rvdw                =  1.4
epsilon_rf          =  62.0
; Temperature coupling is on in two groups
Tcoupl              =  Berendsen
tc-grps             =  Protein  Non-Protein
tau_t               =  0.1      0.1
ref_t               =  300      300
; Energy monitoring
energygrps          =  Protein SOL NA+
; Pressure coupling is not on
Pcoupl              =  Berendsen
tau_p               =  1.0
compressibility     =  4.5e-5
ref_p               =  1.0

Thanks a lot for your answers.

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