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

Justin Lemkul jalemkul at vt.edu
Mon May 13 13:48:01 CEST 2013

On 5/13/13 5:33 AM, Arunima Shilpi wrote:
> 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
> npt_umbrella.mdp...
> I have   my summary_distance.dat as an attachment

Attachments are not allowed by the list, nor is this one particularly useful in 
any sense to anyone who's not familiar with your exact system.

> 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...

I think you should spend some time familiarizing yourself with published 
literature on this topic.  There is a ton of information out there, and it 
really isn't possible to give someone step-by-step instructions via mailing 
list.  The mailing list archive does have some pieces of information that may be 
useful, but the literature should cover everything you need to know.



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


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