[gmx-users] Autocorrelation times from gmx wham and analyze

[David van der Spoel]

Den 2018-09-05 kl. 13:01, skrev Gmx QA:
> Hi all,
> 
> I am running a series of umbrella sampling simulations of a drug across a
> membrane, with the final aim to determine permeability using the local
> diffusion model.
> 
> I have come across papers where the (necessary) autocorrelation times of
> the mean-squared fluctuation of the coordinates are calculated using gmx
> wham, and this is also what I have done like this:
> 
> gmx wham -if pullf-files.dat -it tpr-files.dat -o -hist -ac -oiact
> 
> 
>   and then the ac-times are written to the file iact.xvg.
> 
> 
> To understand better the procedure however, I also wanted to do a similar
> calculation manually.
> 
> I therefore did this:
> 
> 
> gmx traj -f ../umbrella0.part0001.xtc -s ../umbrella0.tpr -ox
> umbrella0_z_com.xvg -com -nox -noy
> 
> 
>   to extract the z-com-coordinates of the drug molecule for a particular us
> window.
> 
> 
> Then:
> 
> 
> gmx analyze -f umbrella0_z_com.xvg -ac -fitfn exp
> 
> 
> Followed by:
> 
> 
> gmx analyze -f autocorr.xvg  -integrate
> 
> 
> to get what I though was going to be the equivalent acf-time tau. However,
> for this umbrella window gmx wham gives me tau =  2.25 whereas the second
> approach gives a value of 122. What could be the reason for this
> difference? There is some info in cmx wham that says that the act
> calculation is cut at a value of 0.05, and that is something that I haven't
> been able to replicate in my second approach, but any insights are highly
> appreciated.
Technical question first. Are you storing the xtc file with the same 
frequency as the data in the pullx or pullf files?
> 
> 
> Cheers
> 
> /PK
> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se