[gmx-users] Interaction energy..

[Justin Lemkul]

On 10/8/12 6:00 AM, rama david wrote:
> Hi justin,
> I correct command as follow and
>   g_enemat -f ener.edr -groups groups.dat -coul -lj
>
> 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 9 elements
> Last energy frame read 50000 time 10000.000
> Will build energy half-matrix of 2 groups, 9 elements, over 50001 frames
> Segmentation fault (core dumped)
>

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://www.bevanlab.biochem.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

========================================