[gmx-users] Extract van der waals surface atoms coordinates

Justin A. Lemkul jalemkul at vt.edu
Fri Nov 18 16:58:50 CET 2011

Alex Jemulin wrote:
> Dear All
> How can I extract van der waals surface atoms coordinates from MD 
> Trajectory and write them to a file?
> Is it possible with gromacs? And with other tools?

g_sas -i produces a topology of surface atoms, from which you can get atom 
numbers, create an index file, then use g_traj to extract the coordinates of 
those atoms.



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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