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

[rama david]

Hi thank you

Please told me the name of Freely available software on which these FF can
be used ..


Thank you in advance

With best wishes and regards,
Rama david


On Wed, Oct 10, 2012 at 6:26 PM, XAvier Periole <x.periole at rug.nl> wrote:

>
> Nope, but on other softwares.
>
>
> On Oct 10, 2012, at 2:50 PM, rama david wrote:
>
>  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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