[gmx-users] constraint pulling
schlesi at uni-mainz.de
Wed Mar 19 11:03:08 CET 2014
Am 17.03.2014 20:11, schrieb
gromacs.org_gmx-users-request at maillist.sys.kth.se:
>> 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?
> If you're using a constraint to preserve distances along the reaction
> coordinate, there's nothing to de-bias. There is no force constant for
> constraint pulling, so you can't run WHAM on its output. The constraint method
> fixes the distance, whereas the umbrella method is a harmonic bias (which is
> what you need for umbrella sampling, hence the name). If you did the "umbrella
> sampling" with the constraint method, there's nothing you're going to get out of it.
The basic simulations are in both cases similar (as is the idea), but
point (4) and (5) differ somewhat. For the constraint simulations:
4) Where umbrella sampling restraints the distances, one constrains here
the distances. That's all... One thing to note (which goes also to point 3):
In umbrella sampling the system can move somewhat along the reaction
coordinate, with the constraints not -> This mean with the constraint
pulling one should use a smaller spacing then for umbrella sampling.
5) De-bias / Calculate the PMF
For the constraint pulling it's just integrating the constraint force
along your reaction coordinate (in principle) - no WHAM as Justin said:
-> V_pmf = - \int (R -> R_max) F_c(r) dr
Tricky part is your reaction coordinate. The above holds only true if
you have a linear reaction coordinate and the force acts only in one
For more complicate reaction coordinates it becomes more complicate.
For a linear reaction coordinate where the force acts along all three
V_pmf = - \int (R -> R_max) [F_c(r) + 2 k_B T / r ] dr
Easiest way to get evenly spaced configuration is using the pull code
with constraints. If one uses a harmonic (/ umbrella) potential, one has
fluctuations, which might are annoying in that case.
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