[gmx-users] gmx densmap tool for the ensemble of the MD trajectories

James Starlight jmsstarlight at gmail.com
Thu Apr 28 12:14:00 CEST 2016

Dear Gromacs users!

To detect different binding sites of the assosiation between two
proteins during 10 independent md runs I would like to i) combine all
of my MD trajectories together and center the receptor protein {which
is consisted of 10 chains determined as 10 .rtp files  within
topology.top } within the merged trajectory using trjconf and then to
ii) calculate the density map using the gmx densmap tool of the second
(smaller) protein determined in the topology.top as the separate chain
(.rtp).  Any suggestions and advises regarding realization of this
workflow? In particular I am interesting- how using only gromacs tools
(without vmd for instance) to obtain merged trajectory?

Thanks for help!


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