[gmx-users] HYDROGEN BOND EXISTENCE MAP
isheeja at iitb.ac.in
Sat Apr 1 09:30:02 CEST 2017
If I understand correctly pdb file is used for extracting information
about the topology of the molecule..in this case the atom name and type.
so it does not matter at which time point of time in your simulation your
pdb file is generated as long as it is whole molecule.
> Hi gromacs users,
> In the perl script to calculate hydrogen bond %, the command is
> perl plot_hbmap.pl -s structure.pdb -map hbmap.xpm -index hbond.ndx
> What should the structure.pdb file contain?
> How to obtain it?
> At which point of simulations?
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