[gmx-users] About Bond breaking and usage of constraints

vidhya sankar scvsankar_agr at yahoo.com
Wed Sep 12 19:34:05 CEST 2012

Dear justin ,
                        Thank you fro your Reply

                     I am doing MD for  Cyclic poly Peptide With ARG as N-termina and PRO as C-terminal .  I have run pdb2gmx it is oak.  . I have solvated and added ions successfully
But when i Run the Energy Minimization The Bond between  N atom of  ARG and C atom of PRO is broken . 

What  Should i Do To keep this Bond Through entire EM and MD ?    Can i Use Constraints option in topology file

 if i need to use  Constraints option What is the  Syntax  ?  Also The Bond is not constructed between N atom and C atom of terminal ARG and PRO residues in Topology 

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