[gmx-users] water molecules (interfacial)

Justin A. Lemkul jalemkul at vt.edu
Sat Nov 13 14:26:22 CET 2010

atila petrosian wrote:
> Dear Mark and gromacs users
> thanks for your time and attention.
> how to make selection.dat file? what should be in that?
> please clarify this new tool more. how can I obtain what I need (number 
> of water molecules (interfacial) to be within
> 2.4 A distance from both the protein and the ligand during simulation. 
> also, exact numeration of each water being
> in interface between protein and ligand)?

I don't know about g_select, but you can do this with g_dist -dist, as well.



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


More information about the gromacs.org_gmx-users mailing list