[gmx-users] g_wham error
rajat desikan
rajatdesikan at gmail.com
Sun Nov 20 22:24:56 CET 2011
Justin,
Should i turn off charges on the methane molecules? I have left them on.
On Mon, Nov 21, 2011 at 12:32 AM, Justin A. Lemkul <jalemkul at 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 <jalemkul at vt.edu<mailto:
>> jalemkul at 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
>> <rajatdesikan at gmail.com <mailto:rajatdesikan at gmail.com**>
>> <mailto:rajatdesikan at gmail.com
>>
>> <mailto:rajatdesikan at gmail.com**>__>> wrote:
>>
>> Oh lovely...thanks for the quick reply Justin :)...
>>
>>
>> On Sat, Nov 19, 2011 at 10:57 PM, Justin A. Lemkul
>> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>> <mailto:jalemkul at vt.edu <mailto:jalemkul at 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
>> 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<http://vt.edu/Pages/Personal/justin>
>> >
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>> >>
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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> | (540) 231-9080
>> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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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
>>
>> ------------------------------**------------------------------**
>> ------------
>>
>>
>> ------------------------------**------------------------------**
>> ------------
>>
>>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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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
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