On Mon, Nov 21, 2011 at 12:32 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
rajat desikan wrote:
My simulations are for 10 ns in each window. There is a lot of
noise in my wham too. I am enclosing my wham for pullf (the
earlier was pullx) and pmf. They are really looking strange.
Stronger restraint means force constant? >From literature, I
kept it at 3000.
Those plots do look very strange. The PMF is almost a step
function, which is certainly wrong. You may need either more
simulation time or more frequent collection of data points, but at
this stage I can only guess. Not much more I can offer, sorry.
A stronger restraint would mean a stronger force constant, yes, but
if you're using 3000 to restrain simple molecules like methane, I
think there is no need to increase it.
-Justin
On Sun, Nov 20, 2011 at 9:12 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
rajat desikan wrote:
hi Justin
I am not able to tell where the lack of overlap is. This
is the
first wham plot I am looking at. In your tutorial and
literature, the wham plots are so clear. Can you please
help me?
Thanks.
It looks like your first one or two windows were not restrained
sufficiently at the desired distance. The error complains
that bin
2 should have points at 0.366 nm, but it appears neither bin
1 nor
bin 2 satisfy this requirement. Check carefully what you have set
for reference distances and what distances were actually
maintained
during the sampling. You may need a stronger restraint or longer
simulations. How long are the simulations? I see that you're
starting the analysis on data after 2 ns, but how much does
that leave?
-Justin
On Sat, Nov 19, 2011 at 11:50 PM, rajat desikan
<rajatdesi...@gmail.com <mailto:rajatdesi...@gmail.com>
<mailto:rajatdesi...@gmail.com <mailto:rajatdesi...@gmail.com>__>
<mailto:rajatdesi...@gmail.com
<mailto:rajatdesi...@gmail.com>
<mailto:rajatdesi...@gmail.com
<mailto:rajatdesi...@gmail.com>__>__>> wrote:
Oh lovely...thanks for the quick reply Justin :)...
On Sat, Nov 19, 2011 at 10:57 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> wrote:
rajat desikan wrote:
Hi
I am a new gromacs user. I just completed Justin's
umbrella
sampling tutorial. I am doing a PMF
calculation between 2
methane molecules in water. The simulation has run
fine till
the g_wham step. My command is
-- g_wham -it tpr-files.dat -if
pullf-files.dat -o -hist
-unit kCal -b 2000
I get a warning:
WARNING, no data point in bin 2 (z=0.366256) !
You may not get a reasonable profile. Check your
histograms!
and my histogram contains a single peak.
I have pulled my other methane 1 nm away from
the first
methane. I have 15 sampling windows (0.05 nm apart
till 5nm
and then 1 nm apart)...can you please tell me
how to
correct
this?
With 15 windows, you should have 15 histograms.
Plot with:
xmgrace -nxy histo.xvg
It will show you where the lack of sampling is.
-Justin
--
==============================______==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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Department of Biochemistry
Virginia Tech
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-- Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
-- Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
------------------------------____----------------------------__--__------------
-- ==============================____==========
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)
231-9080
http://www.bevanlab.biochem.____vt.edu/Pages/Personal/justin
<http://vt.edu/Pages/Personal/justin>
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Dept. of Chemical Engineering,
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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
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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