[gmx-users] constraint pulling
karami.leila1 at gmail.com
Mon Mar 17 15:52:14 CET 2014
Dear gromacs users
I will use pull = constraint (constraint pulling) for PMF calculations.
There is a tutorial about PMF from Justin in which he used
pull = umbrella (umbrella sampling).
In justin tutorial, step are as follows:
1) preparation of system
2) minimization & equilibration
3) generate configuration
4) umbrella sampling
5) WHAM which gives PMF curve
I conceive in my case (pull = constraint), steps 1, 2 and 3 are similar to
justin case (pull = umbrella). Since, WHAM analyzes output files
generated by umbrella sampling, I have not idea about steps 4 and 5.
I did not know how to obtain PMF curve in my case.
If my notion is wrong, please give me more explanation such that I do
this PMF calculation using constraint pulling method. Please tell me steps
Is there a tutorial about PMF calculation using constraint pulling method?
Any help will highly appreciated
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