[gmx-users] Concerns with g_wham

Jennifer Casey jrcasey20 at gmail.com
Tue Apr 20 00:22:18 CEST 2010

Hello again,

As you mentioned, it makes sense that the starting umbrella potential a in
the equation U = (1/2)K(x-a)^2 should be given in the .tpr file.  I have
looked over the manual and online though, and I still cannot see what
portion of the pull code allows me to define the a.  It seems that maybe
GROMACS just takes the starting distance between the two atoms, and centers
the umbrella potential around that distance?  For instance, my starting
configuration starts with the reference group and pull group 0.28 nm away.
I have turned on the pull code in the .tpr file in order to do an umbrella
sample and it looks like this:

pull = umbrella
pull_geometry = distance
pull_dim = Y Y Y
pull_start = yes
pull_ngroups = 1
pull_group0 = Na+
pull_group1 = I-
pull_rate1 = 0.00
pull_k1 = 5000

I don't see how any of these designate where the bottom of the umbrella
potential well lies (except for maybe pull_start - perhaps setting it to yes
puts centers the umbrella potential on the COM of the system).  So instead,
maybe GROMACS realizes that Na+ and I- start 0.28 nm away, and uses this
value as the center of the umbrella potential.

Is this the case?  Or do one of these pull code designations dictate a?


On Fri, Apr 16, 2010 at 4:20 AM, Jochen Hub <jochen at xray.bmc.uu.se> wrote:

> 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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