[gmx-users] PMF curve
ramezanpour.mohsen at gmail.com
Mon May 30 17:28:48 CEST 2011
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
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 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
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