[gmx-users] Pullx file

Justin A. Lemkul jalemkul at vt.edu
Sat Jul 31 12:45:33 CEST 2010

Aswathy wrote:
> 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.


> 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.
> Thanks,
> -- 
> Aswathy


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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