[gmx-users] PMF when pulling in -Z direction

[nahren manuel]

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 <jalemkul at vt.edu>
To: nahren manuel <meetnahren at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
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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