[gmx-users] About Warning in grompp

vidhya sankar scvsankar_agr at yahoo.com
Sun Sep 23 10:17:16 CEST 2012

Dear  Gromacs users
                                       i am doing NPT Eqlibration for a cyclic peptide 

When I run grompp I have got Warning as follows 

WARNING 1 [file 2KDQ3.top, line 1137]:
  The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H has
  an estimated oscillational period of 1.0e-02 ps, which is less than 5
  times the time step of 2.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.
How to Rectify this Warning?

If i Neglect using -maxwarn 1 option then  have got Segmentation Fault during mdrun

Thanks in Advance

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