Hi,
On Wed, Mar 13, 2019 at 12:07 PM Ruth Helena Tichauer <rhtichau.laas.fr> wrote:
> 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).
Unfortunately that frequency isn't nearly enough for calculating the
velocity autocorrelation function (which decays more on the order of
fs). I usually record velocities every 10 fs or so when calculationg
VAC. You're better off using the 'diffusion' command and good ole
Einstein relation.
>
> 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)>?
The 'maxlag' is the maximum lag you want to calculate the VAC function
for (tau in your equation). This is in general something to keep in
mind when calculation any autocorrelation function - as your lag
increases, the number of data points that go into calculating the
function at that point decreases and the function becomes "noisy". The
'tstep' is just the timestep between frames in ps.
>
> 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)?
This is a much trickier problem - in this case I'd recommend using the
'stfcdiffusion' command, which can calculate diffusion for atoms
within a certain distance (defined by 'upper' and 'lower') from atoms
selected by a mask ('mask2') - see the manual for more details.
-Dan
>
> 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 - 10:30:04 PDT
