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

XAvier Periole x.periole at rug.nl
Wed Oct 10 14:43:53 CEST 2012

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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