[gmx-users] PMF curve
ramezanpour.mohsen at gmail.com
Tue May 31 07:59:02 CEST 2011
On Mon, May 30, 2011 at 10:10 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> mohsen ramezanpour wrote:
>> Dear Dr.Justin
>> There is not any answer?
> Please have a bit of patience. I'm not your personal answer service. You
> just happened to catch me at a good time this morning and I was able to
> respond quickly. I have my own work to do, you know.
Thanks for your reply
No Dr.Justin,I didn't mean this by my question.It was your favour replying
to my questions.
I just thought my question is not logical OR it is answer is not difficult
And I must review articles in this field.just this.
>> On Mon, May 30, 2011 at 7:58 PM, mohsen ramezanpour <
>> ramezanpour.mohsen at gmail.com <mailto:ramezanpour.mohsen at gmail.com>>
>> Yes,you are right
>> I need to do more sampling.But the second attached file was just to
>> transfer my mean :)
> Always provide complete information. I can't get in your head to know
> everything you're thinking. If you want free help, make it easy to help
> you. Hack job files wind up causing confusion and delaying an answer rather
> than providing you with one.
Yes,You are right
> 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?
> I have no idea. Watch your trajectories and see what your ligand is doing
> at these points. Presumably you have a window in which the ligand is bound
> in the protein's active/receptor site, and perhaps after some simulation the
> position moves to arrive at its energy minimum. In general, from a PMF
> curve, the highest point (as long as it's stable) minus the lowest point is
> your DeltaG.
> Because there is a difference about 0.5 kcal/mol .
> So there are some energetic differences in these windows. Watch the
> trajectories to figure out why.
> 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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