[gmx-users] Re: Flat energy profile in g_wham
yakovenko_a at ukr.net
Thu Sep 2 01:26:58 CEST 2010
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.
Let's keep this on the list for now please.
Quoting alexander yakovenko <yakovenko_a at ukr.net>:
> Just to close this topic: pullf do corresponds pullx in *all* my MD
> runs... so what is ideas about g_wham flat line (except low
> population of samples)?
> Alex, I would be happy to provide timely advice and direction in
> exchange for middle-authorship. It would, however, need to go through
> the proper channels in order to get my supervisor's approval. To
> formally propose this, you could send an email to my and copy your
> supervisor and my supervisor (pomes at sickkids.ca). Perhaps you and I
> should hash out what it might look like first though, before bothering
> them. From my side, I would prefer if my contribution was limited to a
> single aspect that could be well defined from the start -- I have had
> too many arrangements spiral out of control into large bodies of work
> when I don;t have time available for it.
> Regarding the "evidences", I am not sure what you mean. If you mean to
> ask how did I know? well, I didn't really until you sent the data from
> the water simulation. I took a look at the numbers and figured it out
> -- but I wanted you to figure it out on your own to learn about the
> process. It's just that I have developed a reductionist strategy to
> debug problems that seems to work well and I've seen enough problems
> to know that figuring out numbers and equations for single snapshots
> is the best way to go. Simple systems too so that you can calulate it
> by hand if you need to.
> I don't think that 10x more data is the solution that you need. You
> should go back to the original data pullf and pullx files and see if
> you can relate the pullf to the pullx there also.
> Finally, let's either hash out an authorship agreement or get this
> back on the mailing list.
> Quoting alexander yakovenko <yakovenko_a at ukr.net>:
>> Thank you Chris! I am really appreciating this.
>> Definitely I would like to consult with you about this method.
>> Actually I have no other choice as need to calculate differences in
>> free energy of protein-DNA binding for wt and mutant and umbrella
>> PMF looks like the only method I can carry this out (Jarzynski
>> approach most probably is too demanding). There is a problem
>> however: I can’t just consume your time. If you agree to consider
>> (just consider!) an option to participate our publication where PMF
>> is used to prove meaning of new distant mutation of MEF2B for
>> cancer, then I wouldn’t fill myself like parasite. It would be
>> rather cooperation which sounds much better, right :)? Don’t worry I
>> am not going to bother you much: I have reasonable amount of
>> computers, satisfactory skills with gromacs, empirical data about
>> mutations so on... a bit experience with PMF is very welcome though.
>> As for pullf I just forgotten to subtract initial displacement, now
>> it fits perfect with pullx (Btw how can you judge about evidences
>> from files I have sent? Just because it is so evident?). As for now
>> I restarted mdruns with 0.2ns pull_nst?out, hope 10 times more
>> points will contribute to g_wham’s confidence.
>> If you do decide to continue along with the method that I suggested,
>> I'll join back in. To this point, I see no indication that you have
>> tried to relate the force to the position for the water runs, which is
>> my standing suggestion to you.
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