[gmx-users] Re[17]: Flat energy profile in g_wham

alexander yakovenko 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)?  
> Regards,  
> Alex  
> 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.  
> Chris.  
> 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.  
>> Regards,  
>> Alex  
>> Alex,  
>> 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.  
>> Chris.  
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