abelius wrote:
Dear Justin,
Thank you for your reply... Just to check if I made any mistakes is the
following procedure acceptable?
1) make NDX file with extra groups RES and Protein_Without_RES
2) add options to the MDP file:
energygrps = RES Protein_Without_RES non-Protein
unconstrained_start = yes ;For mdrun -rerun
3) mdrun -rerun <TRR file> -s <new TPR>
Seems fine to me. Rather than waiting for confirmation, you could always go
ahead and try it :) Gromacs will give an error if there are any problems.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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