[gmx-users] constraint pulling

leila karami 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
needed for

constraint pulling.

Is there a tutorial about PMF calculation using constraint pulling method?

Any help will highly appreciated

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