[gmx-users] Fibril not restrained?

[Angelina Malagodi]

Hello: 

I’m using 2beg.pdb and a modified version of the 2lmn.pdb fibril for several systems. The fibrils are quickly collapsing after the first step of production, even after including the posre restraints are called. I added the restraints by including: 

; Include Position restraint file 
#ifdef POSRES_A
#include “posre_Protein_chain_A.itp
#endif

at the end of the respective chain’s topology. When I visualize the system the initial frame looks like the system is restrained, but the fibrils collapse into a more spherical shape after the next frame. 

Is there anything else I can do to restrain the fibril during production? 

Thank you, 

Angelina