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

rama david ramadavidgroup at gmail.com
Wed Oct 10 14:03:05 CEST 2012

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.

With Best wishes and regards,
Rama David

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