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

[James Lord]

Hi Justin,
Here is the uploaded files on 4share.
http://www.4shared.com/folder/9CgRBgqp/_online.html
Cheers
James

On Sun, Oct 19, 2014 at 2:23 PM, James Lord <jjamesgreen110 at gmail.com>
wrote:

> Hi Diogo,
> Yes that is what I have at the end of top file.
> ps: Sorry Justin I just saw your previous email.
> Cheers
> James
>
> On Sun, Oct 19, 2014 at 2:13 PM, Diogo Martins de Sá <sadiogo at mol.bio.br>
> wrote:
>
>> At the end of your topology file, what molecules do you have written
>> down?
>> You should have something like:
>> Protein
>> Surface
>> SOL
>> Ion (if you needed to equilibrate system)
>>
>>
>> Diogo
>>
>>
>>
>>
>> ----------------------------------------------------------------------------------------------------------
>>  Date: Thu, 16 Oct 2014 12:07:15 -0400
>>  From: Justin Lemkul <jalemkul at vt.edu>
>>  To: gmx-users at gromacs.org
>>  Subject: Re: [gmx-users] How to calculate protein-surface interaction
>>  energy
>>  Message-ID: <543FED33.5010700 at vt.edu>
>>  Content-Type: text/plain; charset=windows-1252; format=flowed
>>
>>
>>
>>  On 10/16/14 11:42 AM, James Lord wrote:
>>  > Hi Justin,
>>  > Sorry for not being clear, I have done the simulation without
>> specifying
>>  > the energygrps, so based on your previous comment I should use mdrun
>> -rerun
>>  > trj.xtc -o energy.edr -pn index.ndx? and in index file define
>> energygrps =
>>  > Protein Surface right?
>>  >
>>  > If not appreciate if you give an example of the command with
>> appropriate
>>  > input output etc.
>>
>>  Create a new .tpr with the .mdp file that specifies the desired
>> energygrps, then:
>>
>>  mdrun -s new.tpr -rerun trj.xtc
>>
>>  -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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>