[gmx-users] Doubt about g_dos

[Varvdekar Bhagyesh Rajendra]

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,

Bhagyesh