[gmx-users] How to calculate protein-surface interaction energy

Justin Lemkul jalemkul at vt.edu
Sun Oct 19 16:26:15 CEST 2014

On 10/19/14 7:26 AM, James Lord wrote:
> Hi Justin,
> Well, I tried clicking three different things that said download, but every
> one of them tried to download software, spam, or charge me money, so I'm
> going to assume that the files you sent me off-list are the same ones
> you've posted here.  If that's not the case, please find a better place to
> share files.  Google Docs works well.
> Thanks Google Docs  will be used for future.
> How many different systems do you have?  You said before you had an
> all-atom surface of polyethylene.  This system is a united-atom layer of
> decane.
> I have protein at different liquid-solid interfaces, and I want to have
> interaction energy of all of them.  I think I explained to you in the email
> with attachment why I am sending this (as I have done so many changes to
> protein-PE that I lost track of them)

Well you now have a reference for what "should" work, so hopefully that is 
helpful.  If the PE system is giving issues, please provide *those* files so 
they can be diagnosed and you can get a solution.  If you're having trouble 
keeping track of your own work, it's fairly helpless for anyone else to try ;)



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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