Moeed wrote:
Hello,
I am trying to get only interaction energies (vdw and electrostatics)
between hexane (C6H14, 20atoms) molecules. I have 125 hexane molecules
in the system. I have added _exclusions section_ at the end of top file
to exclude all nonbonded interactions between atom 1 and all other 20
atoms. Unfortunately, I still have problem monitoring the breakdown of
energies.
Why are exclusions necessary? What do you hope to prove by excluding
interactions between one particular atom and the rest of the molecule? I'm
sorry, but that sounds like complete nonsense to me.
grompp -f em -c Hexane-Stack125.gro -p Hexane-Stack125-excl.top -o
Hexane-Stack125_em >& output.grompp_em
mdrun -s Hexane-Stack125_em -o Hexane-Stack125_em -c
Hexane-Stack125_b4pr -v >& output.mdrun_em
grompp -f md19 -c Hexane-Stack125_b4pr -p Hexane-Stack125-excl.top -o
Hexane-Stack125_md >& output.grompp_md
*mdrun -rerun -*s Hexane-Stack125_md.tpr -o Hexane-Stack125_md.tpr -c
Hexane-Stack125_after_md -v >& output.mdrun_md
-------------------------------------------------------
Program g_energy, VERSION 4.0.7
Source code file: enxio.c, line: 283
Fatal error:
Energy file ener.edr not recognized, maybe different CPU?
What does gmxcheck tell you about the .edr file? What was your g_energy command
line? Are your Gromacs versions consistent between the machine running the
calculation and the one you're using to analyze the .edr file?
*******em output:
Steepest Descents converged to Fmax < 1000 in 1 steps
Potential Energy = -1.06286703814635e+03
Maximum force = 2.02809790403662e+02 on atom 1183
Norm of force = 1.41349547097082e+02
********md output
Program mdrun, VERSION 4.0.7
Source code file: gmxfio.c, line: 737
Can not open file:
rerun.xtc
You have to produce a real trajectory (with reasonable physics!) before trying
to rerun it. The mdrun -rerun flag expects an .xtc file. See mdrun -h and read
about the purpose of this flag in the manual.
<snip>
*; Energy group exclusions
eneegygrp_excl = HEX *
Well, you're not going to get any exclusions using this keyword. You want
"energygrp_excl," not "eneegygrp_excl." If this is what's in your .mdp file,
grompp should have raised an error. I still don't know what exactly you're
trying to do.
<snip>
[ molecules ]
; Compound #mols
Hexane 125
*[ exclusions ]
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20*
Does this even work? The [exclusions] directive should be part of the hexane
[moleculetype] definition. Putting it after the definition of the system means
it doesn't apply to hexane at all. Surely grompp would have raised an error
(something like "invalid order for directive exclusions")?
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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