[gmx-users] Concerns with g_wham
Justin A. Lemkul
jalemkul at vt.edu
Tue Apr 20 00:27:29 CEST 2010
Jennifer Casey wrote:
> 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?
You've got it right. The parameter pull_start dictates whether or not the
starting distance is added to the value of pull_init1. The default for
pull_init1 is zero, so setting "pull_start = yes" tells grompp (and then mdrun)
to "add the COM distance of the starting conformation to pull_init" (per the
manual). So the position of the umbrella is 0.28 (pull_start) + 0 (pull_init1)
= 0.28 nm, in your case.
> On Fri, Apr 16, 2010 at 4:20 AM, Jochen Hub <jochen at xray.bmc.uu.se
> <mailto:jochen at xray.bmc.uu.se>> wrote:
> Jennifer Casey wrote:
> 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
> 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.
> Thank you,
> 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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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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