[gmx-users] Re: boundaries in PMF

[Rebeca García Fandiño]

Yes,
my profile seems normal, the only problem are the units in the x-axis, because I expected them to be in the range of the dimensions of the channel.
I will try if I see differences with the other options you proposed, anyway.
Thanks a lot for your help!!
Best wishes, 
Rebeca.

> Date: Thu, 31 May 2012 15:52:48 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Re: boundaries in PMF
> 
> 
> 
> On 5/31/12 3:51 PM, Rebeca García Fandiño wrote:
> > OK,
> > however, just one point about your last comment:
> >
> >  > I suspect this is why g_wham is finding a range of values only equal to half of
> >  > your expected reaction coordinate; it is considering only the positive
> >  > displacement along the reaction coordinate.
> >
> > It seems like all the channel is explored, not only one half. If g_wham was only
> > considering the positive displacement I should see a profile for just one half
> > of the channel, shouldn´t I? and I can see a profile typical for the entire channel.
> >
> 
> Then perhaps it's just a small g_wham output bug (boundary values).  You didn't 
> mention that your profile looked normal ;)
> 
> -Justin
> 
> -- 
> ========================================
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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