[gmx-users] interaction energy using g_enemat

[Justin Lemkul]

On 7/24/13 7:47 AM, Poojari, Chetan wrote:
> Dear All,
>
> I want to calculate interaction energy per residue.
>
> Below is the command i used:
>
> g_enemat -f strand.edr -groups groups.dat -emat strand_emat.xpm
>
>
> my groups.dat file contains these lines:
>
> 3
> strand1_SER_34
> strand1_THR_36
> strand1_TYR_37
>
>
> When i execute the above g_enemat command i get the below error message:
>
> WARNING! could not find group LJ-SR:strand1_SER_34 -strand1_THR_36  (34,36)in energy file
> WARNING! could not find group Coul-SR:strand1_SER_34 -strand1_TYR_37  (34,37)in energy file
>
>
> My strand.edr file looks like this:
>
> LJ-SR:strand1_SER_34-strand1_THR_36
> Coul-SR:strand1_SER_34-strand1_TYR_37
>
>
>
> Please can I get some suggestions on how to get around this problem.
>

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

-- 
==================================================

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

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