Steven Neumann wrote:
Hey Gmx Users,
I went through Justin tutorial of umbrella sampling with spacing of 0.2 nm:
Time COM distance
0 - 0.5
208 - 0.7
218 - 0.92
225 - 1.119
231 - 1.41
235 - 1.61
239 - 1.81
246 - 2.09
253 - 2.3
261 - 2.51
268 - 2.71
276 - 2.91
289 - 3.11
307 - 3.3
325 - 3.5
348 - 3.7
359 - 3.93
371 - 4.1
388 - 4.3
412 - 4.51
423 - 4.7
450 - 4.92
454 - 5
Together 22 windows. I obtained delatG= -37 kcal/mol
Do you have any clue why is that so far away from the value from
tutorial of -50.5 kcal./mol?
Not really. You don't have the even 0.2-nm spacing that the tutorial calls for,
but I know others have reproduced the value, so it should certainly be possible.
-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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