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

[marcos]

Well, not coiled coil, but I have observed serious distortions in a
all-helix protein with G53A6 and reaction field. Using PME solved the
problem.


Marcos

On Mon, 2009-07-20 at 13:50 +0200, Lory Montout wrote:
> 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
> constrained.
> 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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