[gmx-users] g_enermat: group.dat file

[shivangi nangia]

Hello,

I found the following  posts in the forum related  to g_enemat problems:

(A) year 2001 post:
http://gromacs.5086.x6.nabble.com/using-g-enemat-td4391042.html

(B) year 2013 post:
http://gromacs.5086.x6.nabble.com/interaction-energy-using-g-enemat-td5010085.html

In this post, Justin mentions "I think g_enemat is buggy.  People post the
same issue or slight variants of it
all the time.  My version 4.6 installation fares even worse, as group names
aren't even recognized (set to 'null' for everything).

You can get interaction energies over time using g_energy, but I don't
think
g_enemat currently functions properly.

-Justin "

(C) There is another 2013 post:
http://gromacs.5086.x6.nabble.com/Problem-in-g-enemat-in-Gromacs-4-5-5-td5009607.html

The post (A) from 2001, will that work? or there is some issue related to
g_enemat.

Could you please guide

Thanks,
sxn


On Mon, Feb 10, 2014 at 4:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/10/14, 3:59 PM, shivangi nangia wrote:
>
>> Dear Gromacs users,
>>
>> I have a question regarding the input file group.dat that has to be
>> supplied for using g_enemat.
>>
>> The manual says "With *-groups* a file must be supplied with on each line
>> a
>>
>> group to be used."
>>
>> I need to calculate the interaction energy of each of my protein residue
>> (186 residues) with only tail groups of the bi-layer.
>>
>> I am not sure what exactly to write in the group.dat file: residue
>> numbers?
>> atom/bead (CG) name?
>>
>>
>> Will it use the groups I had in the index file that were incorporated in
>> the .edr file?
>>
>>
> What you need are energygrps in the .mdp file.  g_enemat is only a
> post-processing tool for existing energygrps; it cannot decompose nonbonded
> interactions in the way that you want.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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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