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

[patrick fuchs]

>> 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.
> 
> Indeed. rlist = 0.8 and any kind of electostatic cut-off was acceptable 
> in about the 1980s :-)
Well, this is how the force field was parameterized with the force field 
correction in 2004... But I do agree that G53a6 with RF is 'helix 
unfriendly', never tried it with PME though.

Patrick

> 
> Mark
> 
>> 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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>>
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-- 
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Patrick FUCHS
Dynamique des Structures et Interactions des Macromolécules Biologiques
INTS, INSERM UMR-S665, Université Paris Diderot,
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