[gmx-users] Interaction energy..

[Justin Lemkul]

On 10/6/12 6:26 AM, rama david wrote:
> Hi justin,
>
> I tried as per your suggestion.
>
> command line
>
> g_enemat -f ener.edr -groups groups.dat -temp 310  -nolj -free
>
> the out put is like ,
>
>
>
> Opened ener.edr as single precision energy file
> Will read groupnames from inputfile
> Read 2 groups
> group 0WARNING! could not find group (null):energy-energy (0,0)in energy
> file
> WARNING! could not find group (null):energy-extra34 (0,1)in energy file
> group 1WARNING! could not find group (null):extra34-extra34 (1,1)in energy
> file
>
> Will select half-matrix of energies with 3 elements
> Last energy frame read 50000 time 10000.000
> Will build energy half-matrix of 2 groups, 3 elements, over 50001 frames
> Segmentation fault (core dumped)
>
> why program not work ?? Is it  bug??? or Am I doing any stupid mistake???
>

It might be a bug, but I'm not sure yet.  Please run the command without the 
-free option (and thus without -temp) to further reduce complexity.  Then 
manually add the -coul flag.  It should be set by default, but at this point the 
screen output seems to indicate that no energy terms are being detected.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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