Hi Justin,
If you observe my pulling simulation, you will see that the distances are
(increasing) in the negative.
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)
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
========================================
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