[gmx-users] Pullx file

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sat Jul 31 15:56:19 CEST 2010

Dear Aswathy:

When you post to the list, you should include a description of what  
you eventually want to do. Here's an example of why this is important.  
If you want to make PMF then you must use the values of the pulled  
group. I'm not promoting using SMD to make PMFs, but since it is  
possible, I thought I'd point this out.


-- original message --

Aswathy wrote:

[Hide Quoted Text]
Dear friends,

I have pulled a ligand through the channel. Here i kept one residue at
the mouth of the channel as reference and group1 is one of the atom in
the side chain of the ligand.

Now I have the pullx file,( and here 1dz is the z coordinate of
group1-group0), but here I would like to have z-coordiante of the
ligand(instead of the single atom at the side chain)-group1. Becuase I
beleive , that will give the correct position of the ligand (please
correct me if I am wrong)

Is there any way to do this without running the SMD again?
Use g_traj on your trajectory.


[Hide Quoted Text]
I have plotted the g_dist between the reference group and the ligand.
But that does not take the place of pullx. Please give your suggestions.



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