Dear Daniel,
Thank you so much for providing me detailed insight into this matter.
I’ll carefully check all your suggestions on the manual and I’ll come back to you if I have any further inquiries after trying the analysis you propose.
All the best,
Ruth
> On 13 Mar 2019, at 18:17, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> 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 - 14:00:03 PDT
