[gmx-users] Doubt about constrained NM

Varvdekar Bhagyesh Rajendra bhagyesh.varvdekar at research.iiit.ac.in
Wed May 31 13:23:00 CEST 2017

Dear all,

Is it possible to do constrained Normal Mode Analysis in Gromacs such as a free ligand buried in a constrained protein to study the effects of the binding on the normal modes of ligand? I had tried to used DPOSRES_A, as my protein is chain A, but everytime gromacs throws the error "Constraints present with Normal Mode Analysis, this combination is not supported". 

If indeed it is posssible, what are the suggested settings to be done in mdp file. If no, what are the suggested softwares that can do the same.

Thank you,

Best Regards,

IIIT Hyderabad, India

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