[gmx-users] (no subject)

rose rahmani rose.rhmn93 at gmail.com
Mon Apr 23 23:08:27 CEST 2018


I have a capped amino acid in box of water and ion(but the system is not
charged) and named it initial.gro, i can see some unreal bonds when i open
it with VMD(H atom has 2 bonds!). And when i open it with gaussview C and H
atom where nonbobded and were single atoms around remained bonded
structure.( maybe aminoacid in initial.gro file didn't get well optimized
or anything... )

But when i run nvt, the amino acid structure get real structure and
everything is ok.

I remember Justin said that MD and GROMACS can't make or break bond. So
What happend to my system?

Best regards

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