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?<br>
<br>Here is my umbrella sampling .mdp parameters<br><br>pull = umbrella<br>pull_geometry = distance<br>pull_dim = N N Y<br>pull_start = yes<br>pull_nstxout = 10<br>
pull_nstfout = 10<br>pull_ngroups = 1<br>pull_group0 = r_57<br>pull_group1 = r_C1<br>pull_k1 = 1000<br>pull_init1 = 0<br><br><div class="gmail_quote">
On Mon, May 10, 2010 at 4:50 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
Aswathy wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks for your reply.<br>
<br>
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.<br>
<br>
</blockquote>
<br></div>
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.<br>
<br>
What are your .mdp settings during umbrella sampling?<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks<br>
-Aswathy<div class="im"><br>
<br>
On Mon, May 10, 2010 at 3:05 PM, Thomas Piggot <<a href="mailto:t.piggot@soton.ac.uk" target="_blank">t.piggot@soton.ac.uk</a> <mailto:<a href="mailto:t.piggot@soton.ac.uk" target="_blank">t.piggot@soton.ac.uk</a>>> wrote:<br>
<br>
Hi,<br>
<br>
If you defined the reference (r_57) as part of your channel then<br>
with pull_geometry=distance you will have problems as the distance<br>
between pull_group1 and pull_group0 becomes closer to zero and then<br>
the distance becomes positive again.<br>
<br>
I recently had this with my umbrella sampling simulations. Search<br>
for the discussion of things you can do to address this issue on the<br>
list. To stop this being a problem in the first place you should<br>
have used pull_geometry=position.<br>
<br>
Cheers<br>
<br>
Tom<br>
<br>
Aswathy wrote:<br>
<br>
Can any one help me please? I looking forward to hear from any<br>
of you.<br>
Thank you.<br>
<br>
<br>
On Thu, May 6, 2010 at 1:19 PM, Aswathy <<a href="mailto:ammasachu@gmail.com" target="_blank">ammasachu@gmail.com</a><br></div>
<mailto:<a href="mailto:ammasachu@gmail.com" target="_blank">ammasachu@gmail.com</a>> <mailto:<a href="mailto:ammasachu@gmail.com" target="_blank">ammasachu@gmail.com</a><div><div></div><div class="h5"><br>
<mailto:<a href="mailto:ammasachu@gmail.com" target="_blank">ammasachu@gmail.com</a>>>> wrote:<br>
<br>
Ok i will explain you in detail.<br>
<br>
Initially i pulled the ligand through the protein channel ,<br>
using<br>
the given parameters.<br>
<br>
pull = umbrella<br>
pull_geometry = distance<br>
pull_dim = N N Y<br>
pull_start = yes<br>
pull_nstxout = 10<br>
pull_nstfout = 10<br>
pull_ngroups = 1<br>
pull_group0 = r_57<br>
pull_group1 = r_C1<br>
pull_rate1 = 0.01<br>
pull_k1 = 1500<br>
<br>
Then I extracted the frames from the trajectory using the perl<br>
program provided with tutorial. COM distance I took as nearly<br>
0.12<br>
nm. (But sometimes I failed to obtain frames exactly at that<br>
interval, but took nearly at 0.12). Each frame I used for<br>
Umbrella<br>
sampling for 1ns.<br>
Then I checked histograms for overlapping (Some histograms were<br>
entirely overlapped and I removed that from the list, where ever<br>
gaps i selected new frames and did sampling so that I can get an<br>
evenly distributed histograms , I know this will change the<br>
overall<br>
COM distribution but is there any other way to solve this?) .<br>
<br>
Finally once I obtained reasonably good overlapped histograms, I<br>
plotted PMF using g_wham. The plot was a steeply increasing<br>
potential. How can we get increased PMF even when the ligand is<br>
reached out of the channel?<br>
<br>
<br>
Did I made any mistake any where , I am confused.<br>
<br>
Thank you.<br>
-Aswathy<br>
<br>
<br>
<br>
On Thu, May 6, 2010 at 12:56 PM, Jochen Hub<br>
<<a href="mailto:jochen@xray.bmc.uu.se" target="_blank">jochen@xray.bmc.uu.se</a> <mailto:<a href="mailto:jochen@xray.bmc.uu.se" target="_blank">jochen@xray.bmc.uu.se</a>><br>
<mailto:<a href="mailto:jochen@xray.bmc.uu.se" target="_blank">jochen@xray.bmc.uu.se</a><br>
<mailto:<a href="mailto:jochen@xray.bmc.uu.se" target="_blank">jochen@xray.bmc.uu.se</a>>>> wrote:<br>
<br>
Aswathy wrote:<br>
<br>
<br>
Hi gromacs users,<br>
<br>
I am using Gromacs 4.0.4 package. I am doing SMD of a<br>
ligand<br>
transport through a channel.<br>
<br>
I performed SMD and did umbrella sampling (Thanks to<br>
Justin<br>
for his tutorial). Extracted frames with a window<br>
spacing<br>
interval of ~0.12nm. and did 1ns sampling.<br>
Histograms are<br>
with reasonabvle overlap. Then I used g_wham for plotting<br>
PMF considering first 300ps as equilibration.<br>
<br>
Isn't SMD usually referred to pulling at some finite pulling<br>
speed? That would not be umbrella sampling.<br>
<br>
Anyway, you'll have to provide a lot more data to enable<br>
us to<br>
help you.<br>
<br>
Jochen<br>
<br>
<br>
<br>
<br>
I am getting a plot , but potential is increasing<br>
constantly. ie, PMF is not converged as mentioned the<br>
tutorial? Do I need to extend the sampling ? or any other<br>
reason?<br>
<br>
Please help me.<br>
Thank you.<br>
<br>
-Aswathy<br>
<br>
<br>
<br>
-- ---------------------------------------------------<br>
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Molecular Biophysics group<br>
Dept. of Cell & Molecular Biology<br>
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</div></blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Aswathy<br>