Dear amber users and developers,
I wish to compute the velocity autocorrelation function (VACf) of water molecules within the cavity of a protein-ligand complex. I wish to use the usevelocity keyword as in
http://archive.ambermd.org/201605/0236.html <
http://archive.ambermd.org/201605/0236.html> but I haven’t saved any velocity information while running the calculations.. Is there a straightforward manner to re-calculate these velocities from the .nc trajectory file (using cpptraj perhaps)? FYI the trajectories I wish to analyse are 10ns long such that frames were recorded every 1 ps (I wonder if this sampling is enough).
Aside, when reading the manual concerning the velocityautocorr analysis, it is not clear to me what the maxlag is.. Neither what tstep refers to: is it the time difference for computing the autocorrelation i.e the tau in <v(t)v(t+tau)>?
As the VACf is computed for a mask of atoms, and as I wish to get an estimate of the diffusion coefficient of water molecules when they are in the protein cavity (to see if this value is different from the bulk), should I select water molecules within the cavity only (I guess so)? If yes, as they exchange during the simulated time with water molecules from the bulk, should I account for the portions of the trajectory during which they are inside the cavity only (I also suppose yes so but I rather ask)?
Any help concerning any of the previous points will be much appreciated.
Thanking you in advance,
Sincerely,
Ruth
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Received on Wed Mar 13 2019 - 09:30:03 PDT
