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
--
---------------------------------------------------
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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