[gmx-users] Dihedral restraints

Adriana Garro adrianagarrosl at gmail.com
Tue Nov 18 16:38:04 CET 2014

Dear gromacs users,

I am working in a system composed by a protein in a solvated box. It is a
coarse-grained model (Martini ff). The protein has an amyloid part
(strand-loop-strand), at first I tried to simulated this without restraints
but the structure collapsed, then I used position restraints as a result it
kept the structure but due to the type of restraint I applied it is fix in
the box  without possibility of motion (translate, rotate). I was reading
and maybe using dihedral restraints I can solve this problem. Someone knows
if it is possible?
In summary, what I want is keep the amyloid part in its correct structure
but allow its movement within the box.
Thanks in advance!


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