[gmx-users] A small Questions of umbrella samping

[vg]

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