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

[James Lord]

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)

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.

If it is correct (which when I plot the energy it is not) then I will
correct the protein-PE ones.

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.
Cheers
James

-Justin

On Sun, Oct 19, 2014 at 4:18 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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