[gmx-users] About Energy Minimisation

vidhya sankar scvsankar_agr at yahoo.com
Wed Sep 19 12:55:47 CEST 2012

Dear  Mark Thank you for your previous help


                                  With your Help I Have successfully Constructed .top and .gro for my cyclic peptide  After That i Have solvated and  added ions . . But when I do Energy Minimization  My Molecule after Energy Minimization ( I have Visualized .gro file in VMD)   The bond Between N atom of first  Residue ( N-terminal)  and C atom of last residue (C-terminal end)  Has become Broken . How to Avoid this ? 

Thanks in Advance

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