nahren manuel wrote:
Hi Justin,
If you observe my pulling simulation, you will see that the distances
are (increasing) in the negative.
Exactly as you expect. You're pulling along the -Z dimension, as you said
before. So the ligand is pulled from the protein to an increasingly negative
position.
Here is the PMF (image):
http://www.flickr.com/photos/nahrenmascarenhas/6312990056/
this is not one expects in ligand unbinding. (of course these are from
my initial simulations, approx. 1 ns runs in 5 windows)
Don't base any conclusions on what you see. The simulation time and number of
windows are both woefully insufficient to make any reliable observations. Only
once you have done a proper set of umbrella sampling windows will you be able to
tell what's going on. You should also be doing error estimates when computing
the PMF; I suspect the error bars will be as wild as the values in the PMF plot.
-Justin
Best,
nahren
------------------------------------------------------------------------
*From:* Justin A. Lemkul <[email protected]>
*To:* nahren manuel <[email protected]>; Discussion list for GROMACS
users <[email protected]>
*Sent:* Friday, November 4, 2011 7:44 PM
*Subject:* Re: [gmx-users] PMF when pulling in -Z direction
nahren manuel wrote:
> Dear Gromacs Users,
>
> I am trying to study ligand unbinding adopting Umbrella sampling
(using Gmx 4.5.3). during my initial pull to generate configurations for
umbrella windows I have pulled in the -Z direction,
> @ s0 legend "0 Z"
> @ s1 legend "1 dZ"
> 0.0000 7.37361 -0.33625
> 0.0200 7.37377 -0.33631
> 0.0400 7.37404 -0.33637
> 0.0600 7.3744 -0.33643
> 0.0800 7.37473 -0.33649
> .
> .
> .
> .
> 321.0800 7.37523 -1.29949
> 321.1000 7.37442 -1.29955
> 321.1200 7.37374 -1.29961
> 321.1400 7.37355 -1.29967
> 321.1600 7.37404 -1.29973
> 321.1800 7.37491 -1.29979
> 321.2000 7.3757 -1.29985
> 321.2200 7.37608 -1.29991
> 321.2400 7.37595 -1.29997
> 321.2600 7.37518 -1.30003
> 321.2800 7.37395 -1.30009
> .
> .
> .(so on)
>
> Now when I ran simulations in each umbrella windows, the PMF energies
are in negative. My guess is that this is due to my initial setup, or
is there something seriously wrong. And if i am right I should get the
correct PMF by taking the negative of this PMF (or is it)??
So your PMF is negative, why is that a problem? A negative binding
energy indicates favorability of binding.
-Justin
> -----
> ; Pull code (pulling simulation)
> pull = constraint
> pull_geometry = distance pull_dim = N N Y
> pull_start = yes pull_ngroups = 1
> pull_group0 = Protein
> pull_group1 = MAL
> pull_rate1 = 0.005 ;
> pull_k1 = 1000 ; kJ mol^-1 nm^-2
> pull_nstxout = 500 ; every 1 ps
> pull_nstfout = 500 ; every 1 ps
>
> -----
>
> ; Pull code (Umbrella simulation)
> pull = umbrella
> pull_geometry = distance ;
> pull_dim = Y Y Y
> pull_start = yes ;
> pull_ngroups = 1
> pull_group0 = Protein
> pull_group1 = MAL
> pull_rate1 = 0.000 ;
> pull_k1 = 1000 ; kJ mol^-1 nm^-2
> pull_nstxout = 500 ; every 1 ps
> pull_nstfout = 500 ; every 1 ps
>
>
> Best,
> nahren
>
>
>
>
>
>
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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