[gmx-users] Interaction energy..

[rama david]

Hi justin,


g_enemat -f ener.edr -groups groups.dat -coul -nolj


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)


Thank you in advance
Rama david.

>
>>
> Let me be a bit more specific again.  I previously suggested there was a
> problem with the -lj flag activating more than one option in the code, so
> that is a potential problem.  I suggested adding -nolj -coul to test this
> theory.  Please use those options (not -coul -lj) and see what happens.
>
> -Justin
>
>
>> On Mon, Oct 8, 2012 at 3:22 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 10/8/12 5:40 AM, rama david wrote:
>>>
>>>  Hi justin,
>>>>
>>>> As per your advice,
>>>>
>>>>    g_enemat -f ener.edr -groups groups.dat -nocoul -nolj
>>>>
>>>>
>>>> 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 0 elements
>>>> Last energy frame read 50000 time 10000.000
>>>> Will build energy half-matrix of 2 groups, 0 elements, over 50001 frames
>>>> Segmentation fault (core dumped)
>>>>
>>>> What is the reason  ???
>>>>
>>>>
>>>>  I told you to add the -coul flag, not -nocoul.  With the above command,
>>> you're explicitly telling g_enemat to not do anything useful.
>>>
>>>
>>> -Justin
>>>
>>> --
>>> ==============================****==========
>>>
>>>
>>> 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<http://vt.edu/Pages/Personal/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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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