Aswathy wrote:
On Mon, May 10, 2010 at 6:29 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Ok . Now I understood. I have one more doubt , as I mentioned to
you, I am using one residue in the extracellular loop as a reference
point. Since this is in the loop, do you think it can be good
reference point (due to th large fluctuatuion in the loop, will it
affect the result)?
A residue with a more predictable position is probably preferable. If the loop
moves a lot (or even somewhat), the umbrella potential will attempt to maintain
the specified reference distance, so you could get spurious forces.
-Justin
Aswathy wrote:
I am pulling through the channel with respect to a single
residue on one "side"(extracellular) of the structure. I have
used pull_geometry = distance & pull_dim = N N Y. From this
what I understood is ligand will pull along the z direction with
respect to the reference group (away from r_57). (i.e from
extracellular to intracellular). Is this correct?
I don't think so. If you are pulling through a channel, using an
extracellular residue as a reference, you will be changing the sign
of the distance, rendering "pull_geometry = distance" useless. For
example, in order to properly calculate the PMF, you have to pull
from the aqueous solvent, into the channel, then back out into the
solvent. At some point, your ligand is outside the channel (such
that, for example, the z-coordinate of the ligand is greater than
that of r_57, so distance > 0). Then, as your ligand enters the
channel, its z-coordinate is less than that of r_57, so distance <
0. If this is the case, you must use "pull_geometry = position" to
get the correct signs, otherwise your umbrella sampling window
reference distances will be nonsensical.
-Justin
Here is my umbrella sampling .mdp parameters
pull = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = yes
pull_nstxout = 10
pull_nstfout = 10
pull_ngroups = 1
pull_group0 = r_57
pull_group1 = r_C1
pull_k1 = 1000
pull_init1 = 0
On Mon, May 10, 2010 at 4:50 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Aswathy wrote:
Thanks for your reply.
In this case reference (r57) is not the part of the channel.
But it is a residue in the loop above the channel entry.
Thats
why I used pull_geometry=distance. Therefore I am pulling the
ligand away from this reference.
So you are not pulling through the channel? Or you are pulling
through the channel with respect to a single residue on one
"side"
of the structure? If your ligand ever crosses over this
reference
in any way, the reference distance will change sign and thus
Tom is
right, you should use "pull_geometry = position." With
"distance,"
you can only ever have positive reference distances.
What are your .mdp settings during umbrella sampling?
-Justin
Thanks
-Aswathy
On Mon, May 10, 2010 at 3:05 PM, Thomas Piggot
<t.pig...@soton.ac.uk <mailto:t.pig...@soton.ac.uk>
<mailto:t.pig...@soton.ac.uk <mailto:t.pig...@soton.ac.uk>>
<mailto:t.pig...@soton.ac.uk
<mailto:t.pig...@soton.ac.uk> <mailto:t.pig...@soton.ac.uk
<mailto:t.pig...@soton.ac.uk>>>> wrote:
Hi,
If you defined the reference (r_57) as part of your
channel then
with pull_geometry=distance you will have problems as the
distance
between pull_group1 and pull_group0 becomes closer to zero
and then
the distance becomes positive again.
I recently had this with my umbrella sampling
simulations. Search
for the discussion of things you can do to address
this issue
on the
list. To stop this being a problem in the first place
you should
have used pull_geometry=position.
Cheers
Tom
Aswathy wrote:
Can any one help me please? I looking forward to hear
from any
of you.
Thank you.
On Thu, May 6, 2010 at 1:19 PM, Aswathy
<ammasa...@gmail.com <mailto:ammasa...@gmail.com>
<mailto:ammasa...@gmail.com <mailto:ammasa...@gmail.com>>
<mailto:ammasa...@gmail.com
<mailto:ammasa...@gmail.com> <mailto:ammasa...@gmail.com
<mailto:ammasa...@gmail.com>>>
<mailto:ammasa...@gmail.com <mailto:ammasa...@gmail.com>
<mailto:ammasa...@gmail.com <mailto:ammasa...@gmail.com>>
<mailto:ammasa...@gmail.com
<mailto:ammasa...@gmail.com>
<mailto:ammasa...@gmail.com
<mailto:ammasa...@gmail.com>>>>> wrote:
Ok i will explain you in detail.
Initially i pulled the ligand through the protein
channel ,
using
the given parameters.
pull = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = yes
pull_nstxout = 10
pull_nstfout = 10
pull_ngroups = 1
pull_group0 = r_57
pull_group1 = r_C1
pull_rate1 = 0.01
pull_k1 = 1500
Then I extracted the frames from the trajectory
using
the perl
program provided with tutorial. COM distance I
took as
nearly
0.12
nm. (But sometimes I failed to obtain frames
exactly
at that
interval, but took nearly at 0.12). Each frame
I used for
Umbrella
sampling for 1ns.
Then I checked histograms for overlapping (Some
histograms were
entirely overlapped and I removed that from the
list,
where ever
gaps i selected new frames and did sampling so
that I
can get an
evenly distributed histograms , I know this will
change the
overall
COM distribution but is there any other way to
solve
this?) .
Finally once I obtained reasonably good overlapped
histograms, I
plotted PMF using g_wham. The plot was a steeply
increasing
potential. How can we get increased PMF even
when the
ligand is
reached out of the channel?
Did I made any mistake any where , I
am confused.
Thank you.
-Aswathy
On Thu, May 6, 2010 at 12:56 PM, Jochen Hub
<joc...@xray.bmc.uu.se
<mailto:joc...@xray.bmc.uu.se> <mailto:joc...@xray.bmc.uu.se
<mailto:joc...@xray.bmc.uu.se>>
<mailto:joc...@xray.bmc.uu.se
<mailto:joc...@xray.bmc.uu.se> <mailto:joc...@xray.bmc.uu.se
<mailto:joc...@xray.bmc.uu.se>>>
<mailto:joc...@xray.bmc.uu.se
<mailto:joc...@xray.bmc.uu.se>
<mailto:joc...@xray.bmc.uu.se <mailto:joc...@xray.bmc.uu.se>>
<mailto:joc...@xray.bmc.uu.se
<mailto:joc...@xray.bmc.uu.se>
<mailto:joc...@xray.bmc.uu.se
<mailto:joc...@xray.bmc.uu.se>>>>> wrote:
Aswathy wrote:
Hi gromacs users,
I am using Gromacs 4.0.4 package. I am
doing
SMD of a
ligand
transport through a channel.
I performed SMD and did umbrella sampling
(Thanks to
Justin
for his tutorial). Extracted frames
with a window
spacing
interval of ~0.12nm. and did 1ns sampling.
Histograms are
with reasonabvle overlap. Then I used
g_wham
for plotting
PMF considering first 300ps as
equilibration.
Isn't SMD usually referred to pulling at some
finite pulling
speed? That would not be umbrella sampling.
Anyway, you'll have to provide a lot more
data to
enable
us to
help you.
Jochen
I am getting a plot , but potential is
increasing
constantly. ie, PMF is not converged as
mentioned the
tutorial? Do I need to extend the
sampling ?
or any other
reason?
Please help me.
Thank you.
-Aswathy
--
---------------------------------------------------
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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-- Aswathy
-- Aswathy
-- Dr Thomas Piggot
University of Southampton, UK.
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-- Aswathy
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
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Aswathy
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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