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 <[email protected]> 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
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