[gmx-users] Concerns with g_wham

[Jochen Hub]

Jennifer Casey wrote:
> Hello,
>
> I have been using g_wham, but I have a few questions that I can't find 
> answers to online.  When using WHAM, one does not need the forces 
> between the pull groups to calculate the PMF, yet g_wham won't run 
> without it.  Is there a reason for this?
Hi Jennifer!

As pointed out by Chris, you can use provide the pull positions (g_wham 
-ix) OR the pull forces with -if. When giving the pullf files, g_wham 
simply computes the pull positions from the forces and calculates the 
histograms etc...

>
> Also, when using the pull code, I am allowed to define the spring 
> constant K for umbrella sampling, but I do not designate where the 
> umbrella potential is centered.  How does gromacs determine this?
Umbrella positions and force constants (and pull geometry) are taken 
from the tpr files. That's why they must be provided to g_wham.

> I am interested as I would like to create a PMF using umbrella 
> integration (from code I will write myself) rather than use WHAM.  To 
> do this and still use the umbrella sampling runs used with GROMACS, I 
> need to know where my umbrella potentials are centered.
If you want to integrate the mean forces, I would not use pull=umbrella 
but pull=constraint. You should get the same PMF compared to umbrella 
sampling and using g_wham.

Please let me know if g_wham makes any trouble.

Cheers,

Jochen
>
> Thank you,
> Jennifer


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Dr. Jochen Hub
Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755
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