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

[Justin A. Lemkul]

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
> 
> 
> 
> 
> 
> 

-- 
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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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