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

[Justin Lemkul]

On 10/18/14 10:41 PM, James Lord wrote:
> Hi Justin,
> Here is the uploaded files on 4share.
> http://www.4shared.com/folder/9CgRBgqp/_online.html

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.

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.  If you 
want people to spend time helping you, you need to provide accurate information. 
  This system behaves correctly - there is a zero interaction energy (both 
Coulomb and LJ) at t=0, so it is fine.  But I don't know what I'm supposed to be 
spending my time doing, because this isn't the system you described before as 
being problematic.

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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