[gmx-users] Martini FF for Sec structure changes...

[rama david]

Thank you for your reply,

Are these Cg can be used in Gromacs.

Thank you in advance.

With best wishes and regards,

Rama david

On Wed, Oct 10, 2012 at 6:13 PM, XAvier Periole <x.periole at rug.nl> wrote:

>
> Martini FF cannot model changes in secondary structure ... other CG FF
> can. You'll find them easily in the literature. Notably the ones from
> Deserno or Derreumaux.
>
>
> On Oct 10, 2012, at 2:03 PM, rama david wrote:
>
>  Hi friends,
>>
>> I planed to use the martini force-field for my simulation study of
>> peptide.
>>
>> The peptides are initially alpha-helix in nature. As they come together
>> they formed amyloid fibre( Antiparallel Beta structure).
>>
>> Is it is possible to study the secondary structure backbone study by
>> martini force field.????
>>
>> I read in there tutorial that the Secondary structure is predefined
>> therefore they are statics through out the simulation.
>> Conformational changes that  produces  changes in Sec structure are out of
>> scope in martini. only  tertiary structure are free defined to change..
>>
>>
>> So what to do ???
>> How to use Martini FF to study secondary structure ???
>>
>> Is there any way to use coarse grained FF to use for study in Sec.
>> structure???
>>
>>
>> With Best wishes and regards,
>> Rama David
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