[gmx-users] PMF curve

[mohsen ramezanpour]

Dear Dr.Justin

There is not any answer?


On Mon, May 30, 2011 at 7:58 PM, mohsen ramezanpour <
ramezanpour.mohsen at gmail.com> wrote:

> Yes,you are right
> I need to do more sampling.But the second attached file was just  to
> transfer my mean :)
> My final PMF curve is the first attached file.
>
> Sorry for asking more questions..
>
> Regarding my notes about windowses in last email and looking at FIRST
> attached file:
> Which one is my starting point?
> 0.18 (with negative value ) OR 0.03 (with about zero value) OR the average
> in that region?
>
> Because there is a difference about  0.5 kcal/mol .
> Thanks in advance
>
>
>
>
>
> On Mon, May 30, 2011 at 7:42 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> mohsen ramezanpour wrote:
>>
>>> Thank you.
>>>
>>> no,I think the problem is not zero point.
>>> Actually I maean some thing like this one.please have a look at new
>>> attached file.
>>> I just added 3 new windows in 0.3 - 0.8
>>> But the whoe of my curve shifted upward.
>>>
>>> There is another question:
>>> Actually I pulled my drug from 0.18 - 3.18
>>> then,extracted some windows.umbrella0 for 0.18 and umbrella20 for 3.18
>>> Besides as we know drug is oscilating in it's windows.
>>> so ,it must cover places as like as 0.12 and 3.22 too.
>>> Am I right?
>>>
>>>
>> Possibly.  Harmonic potentials allow for oscillation.  The amount by which
>> the position shifts is a function of both the force constant you apply and
>> the nature of the interactions within the system.
>>
>>
>>  But looking at curve it seems my drug couln't cover the region around
>>> 0.18
>>> besides it ha covered completely(untill 0.03) the region around 0.18
>>>
>>> What is the problem?
>>>
>>> Since I started from 0.18 (which energy is negative there),I am in doubt
>>> about starting point.
>>> Because it can be eighter 0.03 OR 0.18
>>>
>>>
>> All of this appears to be a consequence of poor sampling.  You have
>> several flat locations in both the PMF curves, indicating absolutely no
>> sampling in that region.  Your histograms should show you this, as well.
>>  You need more windows and more time in each.  Based on what you've shown,
>> your simulations are simply unconverged.
>>
>>
>> -Justin
>>
>> --
>> ========================================
>>
>> 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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>
>
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