Dear Justin
thank you for your reply.
i have thought about the possibility you said before, but some paper make me
confuse.
the paper at: dx.doi.org/10.1021/ja303286e | J. Am. Chem. Soc. 2012, 134,
10959−10965 and PLOS Computational Biology | www.ploscompbiol.org 3 January
2014 | Volume 10 | Issue 1 | e1003417.
they use CGMD simulation to calculate PMF of two big protein in the membrane,
the PMF image which they get also have a steep increase
at small values along the reaction coordinate. so, why?
i put these figures at:
https://t.williamgates.net/thumb-4EA4_5482C129.jpg
https://t.williamgates.net/thumb-FA03_5482C129.jpg
https://t.williamgates.net/thumb-E3CB_5482C129.jpg
https://t.williamgates.net/thumb-F117_5482C4F9.jpg
Cao
Dear gromacs users
I read the tutorial of umbrella sampling and have a small question I don't know
I do a umbrella samping simulation as the tutorial show us, the pmf image also
like the tutorial result .
But I was read another papers like the explain paper of g-wham: JCTC 2010.6
3713-3720. The pmf image have a immediately move up in figure 1&2 。
How could I get the pmf image like this? do I need to take more window in the
high energy barrier position or just use some commands behind the g-wham or
modify the map file ?
Look forward reply and thank you very much
P.S. i take the two figure in attachment please check.
Your sincerely Cao
China ,TianJin, Nanking university
School of physics
Ph.d
发自我的 iPad
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
