[gmx-users] PMF of ligand transport

[Thomas Piggot]

Hi,

If you defined the reference (r_57) as part of your channel then with 
pull_geometry=distance you will have problems as the distance between 
pull_group1 and pull_group0 becomes closer to zero and then the distance 
becomes positive again.

I recently had this with my umbrella sampling simulations. Search for 
the discussion of things you can do to address this issue on the list. 
To stop this being a problem in the first place you should have used 
pull_geometry=position.

Cheers

Tom

Aswathy wrote:
> Can any one help me please? I looking forward to hear from any of you.
> Thank you.
> 
> 
> On Thu, May 6, 2010 at 1:19 PM, Aswathy <ammasachu at gmail.com 
> <mailto:ammasachu at gmail.com>> wrote:
> 
>     Ok i will explain you in detail.
> 
>      Initially i pulled the ligand through the protein channel , using
>     the given parameters.
> 
>     pull                     = umbrella
>     pull_geometry            = distance
>     pull_dim                 =  N N Y
>     pull_start               = yes
>     pull_nstxout             =  10
>     pull_nstfout             =  10
>     pull_ngroups             =  1
>     pull_group0              =  r_57
>     pull_group1              =  r_C1
>     pull_rate1               =  0.01
>     pull_k1                  =  1500
> 
>     Then I extracted the frames from the trajectory using the perl
>     program provided with tutorial. COM distance I took as nearly 0.12
>     nm. (But sometimes I failed to obtain frames exactly at that
>     interval, but took  nearly at 0.12). Each frame I used for Umbrella
>     sampling for 1ns.
>     Then I checked histograms for overlapping (Some histograms were
>     entirely overlapped and I removed that from the list, where ever
>     gaps i selected new frames and did sampling so that I can get an
>     evenly distributed histograms , I know this will change the overall
>     COM distribution but is there any other way to solve this?) .
> 
>     Finally once I obtained reasonably good overlapped histograms, I
>     plotted PMF using g_wham. The plot  was a steeply increasing
>     potential.  How can we get increased PMF even when the ligand is
>     reached out of the channel?
> 
> 
>  
> 
>     Did I made any mistake any where , I am confused.
> 
>     Thank you.
>     -Aswathy
> 
> 
> 
>     On Thu, May 6, 2010 at 12:56 PM, Jochen Hub <jochen at xray.bmc.uu.se
>     <mailto:jochen at xray.bmc.uu.se>> wrote:
> 
>         Aswathy wrote:
> 
> 
>             Hi gromacs users,
> 
>             I am using Gromacs 4.0.4 package. I am doing SMD of a ligand
>             transport through a channel.
> 
>             I performed SMD and did umbrella sampling (Thanks to Justin
>             for his  tutorial). Extracted frames with a window spacing
>             interval  of ~0.12nm. and did 1ns sampling. Histograms are
>             with reasonabvle overlap. Then I used g_wham for plotting
>             PMF considering first 300ps as equilibration.
> 
>         Isn't SMD usually referred to pulling at some finite pulling
>         speed? That would not be umbrella sampling.
> 
>         Anyway, you'll have to provide a lot more data to enable us to
>         help you.
> 
>         Jochen
> 
> 
> 
> 
>             I am getting a plot , but potential is increasing
>             constantly. ie, PMF is not converged as mentioned the
>             tutorial? Do I need to extend the sampling ? or any other
>             reason?
> 
>             Please help me.
>             Thank you.
> 
>             -Aswathy
> 
> 
> 
>         -- 
>         ---------------------------------------------------
>         Dr. Jochen Hub
>         Molecular Biophysics group
>         Dept. of Cell & Molecular Biology
>         Uppsala University. Box 596, 75124 Uppsala, Sweden.
>         Phone: +46-18-4714451 Fax: +46-18-511755
>         ---------------------------------------------------
> 
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> 
> 
> 
>     -- 
>     Aswathy
> 
> 
> 
> 
> -- 
> Aswathy
> 

-- 
Dr Thomas Piggot
University of Southampton, UK.