[gmx-users] Center of Mass (COM) spacing between protein and ligand

Arunima Shilpi writetoash28 at gmail.com
Mon May 13 11:33:45 CEST 2013

Respected Sir
many many thanks for your reply to my last mail. I was able able to debug
the error

Here I have new set of queries..

How much COM spacing should i consider for my protein-ligand interactiom
How much total distance I should move along z-axis/...
and which all conf file should i take into consideration for

I have   my summary_distance.dat as an attachment

Here in your example I could not understand as to why have you taken conf0
extending to con450 for ur npt_umbrella.mdp..

I request you to kindly guide me to the next step...


Thanking You with Regards.

Arunima Shilpi

Ph. D Research Scholar(Cancer & Epigenetics)
Department of Life Science
National Institute of Technology

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