[gmx-users] Umbrella sampling histograms.

[rose rahmani]

Hi,

I did umbrella sampling for different distances of amino acid  above
surface.
I found i special distance (1-1.2 nm above surface)histograms  does not
overlap. I did the sampling several times even for each 0.001 nm( of the
distane between 1-1.2 nm) but the histo.xvg file didn't show ANY changes in
that distance.
When you see in histo.xvg file that there isn't any data in 1nm, is that
really 1nm??? Because the histo file begins and ends  from 0.8 difference
in comparision to real distances. I MEAN, i choosed distances between 1nm
and 1.7 nm to sample. But histogram shows the windows from 0.2 nm to 1.78
nm. I think it's normal because each curve have width so when i choose 1nm
infact gives histo between 0.6 to 1.4 which depends to force constant.is it
true?


 My question is that:
1- in my case i don't have any curve in 1-1.2 nm. Should i choose really
distances 1 to 1.2 nm from summarydistances file?

2- as i told before, i sample different distances between 1-1.2, but i
couldn't find any change in histo.xvg file and for profile.xvg file at 1.1
nm there is an odd number for energy(too high)  which shows the discrepency
and discontinuity in sampling.

3-does it mean the amino acid doesn't stay in 1-1.2 nm? If yes, so why i
see this distance in summarydistances.dat file?

Maybe my explanation is  a little bit confusing;) but hope to be clear...


Best regards