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

[Mark Abraham]

marcos wrote:
> 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 :-)

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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