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A solution of that thread: g_wham do not integrate properly is some part of profile covered with only a window. Particularly I was ale to integrate http://picasaweb.google.ca/117558205101329348732/G_wham#5511244561053627250 with options -min 4.1 -max 5.8. With wider borders it's profile turns into flat line.
<br />Regards,
<br />Alex.
<br />
<br />
<br />
<blockquote class="ukr_editor_quotation" style="border-left: 1px solid rgb(204, 204, 204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;">Let's keep this on the list for now please.
<br />
<br />Quoting alexander yakovenko <yakovenko_a@ukr.net>:
<br />
<br />> Just to close this topic: pullf do corresponds pullx in *all* my MD
<br />> runs... so what is ideas about g_wham flat line (except low
<br />> population of samples)?
<br />> Regards,
<br />> Alex
<br />>
<br />>
<br />>
<br />> Alex, I would be happy to provide timely advice and direction in
<br />> exchange for middle-authorship. It would, however, need to go through
<br />> the proper channels in order to get my supervisor's approval. To
<br />> formally propose this, you could send an email to my and copy your
<br />> supervisor and my supervisor (pomes@sickkids.ca). Perhaps you and I
<br />> should hash out what it might look like first though, before bothering
<br />> them. From my side, I would prefer if my contribution was limited to a
<br />> single aspect that could be well defined from the start -- I have had
<br />> too many arrangements spiral out of control into large bodies of work
<br />> when I don;t have time available for it.
<br />>
<br />> Regarding the "evidences", I am not sure what you mean. If you mean to
<br />> ask how did I know? well, I didn't really until you sent the data from
<br />> the water simulation. I took a look at the numbers and figured it out
<br />> -- but I wanted you to figure it out on your own to learn about the
<br />> process. It's just that I have developed a reductionist strategy to
<br />> debug problems that seems to work well and I've seen enough problems
<br />> to know that figuring out numbers and equations for single snapshots
<br />> is the best way to go. Simple systems too so that you can calulate it
<br />> by hand if you need to.
<br />>
<br />> I don't think that 10x more data is the solution that you need. You
<br />> should go back to the original data pullf and pullx files and see if
<br />> you can relate the pullf to the pullx there also.
<br />>
<br />> Finally, let's either hash out an authorship agreement or get this
<br />> back on the mailing list.
<br />>
<br />> Chris.
<br />>
<br />> Quoting alexander yakovenko <yakovenko_a@ukr.net>:
<br />>
<br />>>
<br />>>
<br />>> Thank you Chris! I am really appreciating this.
<br />>>
<br />>> Definitely I would like to consult with you about this method.
<br />>> Actually I have no other choice as need to calculate differences in
<br />>> free energy of protein-DNA binding for wt and mutant and umbrella
<br />>> PMF looks like the only method I can carry this out (Jarzynski
<br />>> approach most probably is too demanding). There is a problem
<br />>> however: I can’t just consume your time. If you agree to consider
<br />>> (just consider!) an option to participate our publication where PMF
<br />>> is used to prove meaning of new distant mutation of MEF2B for
<br />>> cancer, then I wouldn’t fill myself like parasite. It would be
<br />>> rather cooperation which sounds much better, right :)? Don’t worry I
<br />>> am not going to bother you much: I have reasonable amount of
<br />>> computers, satisfactory skills with gromacs, empirical data about
<br />>> mutations so on... a bit experience with PMF is very welcome though.
<br />>>
<br />>> As for pullf I just forgotten to subtract initial displacement, now
<br />>> it fits perfect with pullx (Btw how can you judge about evidences
<br />>> from files I have sent? Just because it is so evident?). As for now
<br />>> I restarted mdruns with 0.2ns pull_nst?out, hope 10 times more
<br />>> points will contribute to g_wham’s confidence.
<br />>>
<br />>> Regards,
<br />>>
<br />>> Alex
<br />>>
<br />>>
<br />>>
<br />>>
<br />>>
<br />>>
<br />>>
<br />>>
<br />>> Alex,
<br />>>
<br />>> If you do decide to continue along with the method that I suggested,
<br />>> I'll join back in. To this point, I see no indication that you have
<br />>> tried to relate the force to the position for the water runs, which is
<br />>> my standing suggestion to you.
<br />>>
<br />>> Chris.
<br />>>
<br />>>
<br />>>
<br />
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