[gmx-users] PMF of ligand transport

Aswathy ammasachu at gmail.com
Thu May 6 09:49:43 CEST 2010

Ok i will explain you in detail.

 Initially i pulled the ligand through the protein channel , using the given

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 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 with some small
curves here and there. The PMF is not at all converged. Did I made any
mistake any where , I am confused. If you want I can attach the PMF profile

Thank you.

On Thu, May 6, 2010 at 12:56 PM, Jochen Hub <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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