[gmx-users] -ignh correct usage

Sana Saeed bioinformatic.lady at yahoo.com
Wed Jul 22 16:01:47 CEST 2015

"During processing the atoms will be reordered according to GROMACS conventions. With -n an index file can be generated that contains one group reordered in the same way. This allows you to convert a GROMOS trajectory and coordinate file to GROMOS. There is one limitation: reordering is done after the hydrogens are stripped from the input and before new hydrogens are added. This means that you should not use -ignh."
what does this paragraph mean? in last it says we shoulnt use -ignh... but i am confused , what are they trying to say. what is the right use of this option?

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