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

[James Lord]

Hi Justin,
Would you please tell me from the files I sent you which of them you
checked and how you got to the conclusion that  (I mean which command )
"This system behaves correctly - there is a zero interaction energy (both
Coulomb and LJ) at t=0, so it is fine".
Thanks
James

On Mon, Oct 20, 2014 at 3:26 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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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