[gmx-users] boundaries in PMF

[Justin A. Lemkul]

On 5/31/12 1:20 PM, Rebeca García Fandiño wrote:
> Hi,
> I am trying to calculate a PMF for an ion along a channel. Everything went OK,
> but when I used g_wham I got a profile with strange dimensions for the x-axis.
> What are the boundaries g_wham is using for calculating the units of x-axis?
>

The values are based on the restraint distances along the reaction coordinate.

> I have used:
> g_wham -it tpr-files.dat -if pullf-files.dat -o file_output.xvg -hist
> file_histo_output.xvg -unit kCal -cycl yes
>
> (version 4.0.7)
>
> and the units I got in the x-axis are determined by the boundaries:
>
> "Determined boundaries to 0.000035 to 2.603290 "
>
> Which are these units? nm?
>

Yes.

> The z coordinate for my ion explores at least 5 nm!!
>
> I am a bit confused about that.
>

The exact output depends on how you set up the umbrella sampling (in the .mdp 
file).  The range of values corresponds to whatever the distances are that are 
sampled in the various windows.  Perhaps there is a sign issue here?  Do you 
have some restraints that are at negative displacement and others at positive? 
Did you set up the .mdp files properly to account for this behavior?

-Justin

-- 
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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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