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
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