[gmx-users] Doubt about g_dos

Varvdekar Bhagyesh Rajendra bhagyesh.varvdekar at research.iiit.ac.in
Mon Sep 18 20:49:12 CEST 2017

Dear all,

I am attempting to find the Vibrational density of states of protein bound to ligand in a water box using the command g_dos. To do so, should I extract the protein part from the entire trajectory file containing coordinates and velocities of all atoms (trr file) and then run g_dos on the resultant partial trajectory containing only protein coordinates and velocities ? or the entire trajectory which of course doesn't make sense ?

Thank you,


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