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

[XAvier Periole]

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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>>
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