[gmx-users] Interaction energy

[Steven Neumann]

On Tue, Oct 18, 2011 at 11:41 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Steven Neumann wrote:
>
>
>>
>> On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    Steven Neumann wrote:
>>
>>        Dear Gmx Users,
>>         I would like to calculate the interaction energy (LJ and
>>        electrostatic) between each residue and my ligands (10 ligands
>>        in the system). I would like to see what is the contribution of
>>        electrostatic and vdW interactions between ligand and each of my
>>        residue. I thought to use g_energy and specify each of my
>>        residues in index files but it is not possible. Will you suggest
>>        how to do this?
>>
>>
>>    For such information, you have to specify these groups as energygrps
>>    in the .mdp file.  You can rerun the trajectory using mdrun -rerun
>>    and a new .tpr file specifying these groups, but depending on the
>>    output frequency, the result may not be as accurate as you'd like.
>>
>>    -Justin
>>
>>  Thank you Justin. Now I have two groups sepcified in my mdp file:
>>  energygrps = Protein LIG
>>
>> How can I specify each residue of my protein separately and each ligand?
>> In my md.gro file I have residues:
>>
>>    91GLY 92TYR ..... 161LIG 162LIG...
>>
>>  Will it be correct like this
>>  energygrps = 91GLY 92 TYR ... 161LIG 162LIG...
>>
>>
>
> No.  The names must correspond to valid groups in an index file.
>
>
So do you mean that that I should add my index file with


grompp -f md.mdp -c npt.gro -n *index.ndx* -t npt.cpt -p topol.top -o md.tpr



with specified groups in md.mdp file like they are specified in index file?
:) Then just to



mdrun -rerun -deffnm md2



Please, let me know whether I am correct or not.



Steven

>
> If yes, will this simulation take longer? Thank you
>>
>
> Perhaps, but certainly your energy file will be considerably larger.
>
> -Justin
>
>  Steven
>>
>>
>>
>>
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111018/1a42dada/attachment.html>