[gmx-users] analysis of PMF calculations

Rebeca García Fandiño regafan at hotmail.com
Sun Sep 11 23:58:32 CEST 2011

Thanks, Justin. Just one note: the values of min and max are not the same (-min -2.4750 -max 2.4750), they have opposite values. The c.o.m is taken as zero. If they were the same I would understand your suggestion, but they are not, so Gromacs should not understand that the system has zero size, should it?

> Date: Sun, 11 Sep 2011 17:39:55 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] analysis of PMF calculations
> Rebeca García Fandiño wrote:
> > Thanks again, I have uploaded to the version 4.5.4 and instead of zeros 
> > in the second column, I obtain nan, which comes to be the same :-S
> > Sorry, but I am a bit confused about your comments. If I use the option 
> > -cycl (this is what I can read in the Help from Gromacs):
> > 
> > "For cyclic or periodic reaction coordinates (dihedral angle, channel PMF
> > without osmotic gradient), the option -cycl is useful. g_wham will make use
> > of the periodicity of the system and generate a periodic PMF. The first and
> > the last bin of the reaction coordinate will assumed be be neighbors."
> > 
> > If I assume that my channel is periodic (which it is not), I do not get 
> > errors. The problem comes if I assume that it is not periodic, then my 
> > second column is "nan". In a previous mail, you had wrote me:
> > 
> In what way is your channel not periodic?  I'm trying to understand your problem 
> more completely.  I would suspect your issue (judging by previous commands) is 
> that if the value of max and min are the same in the absence of -cycl, then 
> you'll get nonsense as output.  Hence I said:
> >> That makes sense.  You're telling g_wham that you have a PMF starting 
> >> and ending at the same place, but it's not a periodic profile.  It can't 
> >> debias the sampling windows over zero space.
> > 
> > 
> > So, just to get it clear, if I assume that a system that itś not 
> > periodic is periodic (using the option -cycl), I should have problems, 
> > and not the opposite, what itś just what I am observing. Is it not right?
> I still need to know why your system isn't periodic.  From before, using max = 
> min in conjunction with -cycl gives g_wham a reasonable set of parameters to 
> work with.  Having max = min without -cycl is going to fail, because essentially 
> you're telling g_wham that the system has zero size and therefore the reaction 
> coordinate is of zero length (which is why, I suspect, you get "nan" - division 
> by zero).
> > Besides, I have also analyzed analogous PMF results using the same 
> > channel, but another ion (the PMF is for an ion crossing a membrane 
> > channel), and I do not have this type of problem.
> > 
>  From this description, you should indeed have a periodic PMF.  Thus I don't 
> understand the insistence that -cycl shouldn't be used.
> -Justin
> -- 
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110911/bfeb346e/attachment.html>

More information about the gromacs.org_gmx-users mailing list