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.
-Justin
Thanks,
Jennifer
On Fri, Apr 16, 2010 at 4:20 AM, Jochen Hub <[email protected]
<mailto:[email protected]>> 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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
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jalemkul[at]vt.edu | (540) 231-9080
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