Position restraints in mdp file

User discussions
1

-DPOSRES -DPOSRES_FC_BB=400.0 -DPOSRES_FC_SC=40.0 . I want to know the signification of these values (400 and 40). If i change these value what effect will it have on th

2

Hi,
I guess that the topology files are generated by CHARMM-GUI. In that case DPOSRES_FC_BB and POSRES_FC_SC BB stands for the protein BackBone and SC for the protein Side Chains and the values correspond to a force values. But to be sure, you have to look at definition of the position restraints in the topology file. You find it at the end of each [ moleculetype ] directive.

Maybe this tutorial is useful Introduction to Membrane-Protein Simulation — GROMACS tutorials https://tutorials.gromacs.org documentation

Kind regards
Alessandra

3

Hi,
I have seen mdp files generated for a protein-bilayer system by charmm-gui containing position restraints gradually released during multiple equilibration steps. However, I couldn’t find any articles in literature about gradual release of position restraints. Could you please help me to find an article or some reliable source? I want to justify it in my thesis. :D