[gmx-users] energy break down

[Justin A. Lemkul]

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

-- 
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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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