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>> 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>>> 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>>> 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
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Aswathy
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Dr Thomas Piggot
University of Southampton, UK.
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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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