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

[Diogo Martins de Sá]

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
 
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