[gmx-users] calculate avarage and maximum non-bonded energy between energy groups

[Vitaly V. Chaban]

1) g_energy

2) g_analyze -f energy.xvg

3) Divide by 3

I do not know the physical sense of " the maximum interaction energy".





On Mon, Aug 24, 2015 at 4:25 PM, Tushar Ranjan Moharana
<tusharranjanmoharana at gmail.com> wrote:
> Hi everyone,
> I want to calculate the average and if possible maximum non-bonded energy
> between different energy groups. I used gmx energy whose out put was energy
> vs time. I want different energy groups in X axix and energy (average
> and/or maximum) in Y axis. A matrix of N X N describing energy (average
> and/or maximum) between energy groups is also fine. (where N is number of
> energy group).
> I tried gmx enemat but it ends with following error
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> *Opened FOA2_lip_pull.edr as single precision energy fileWill read
> groupnames from inputfileRead 2 groupsgroup 0WARNING! could not find group
> Coul-SR:Protein-Protein (0,0)in energyfileWARNING! could not find group
> LJ-SR:Protein-Protein (0,0)in energy fileWARNING! could not find group
> Coul-SR:Protein-Non-protein (0,1)in energyfileWARNING! could not find group
> LJ-SR:Protein-Non-protein (0,1)in energy filegroup 1WARNING! could not find
> group Coul-SR:Non-protein-Non-protein(1,1)in energy fileWARNING! could not
> find group LJ-SR:Non-protein-Non-protein (1,1)in energyfileWill select
> half-matrix of energies with 0 elementsLast energy frame read 1400 time
> 1400.000Will build energy half-matrix of 2 groups, 0 elements, over 1401
> framesSegmentation fault (core dumped)*
>
> I tried 4.6.7 version and install GROMACS in debug mode but nothing worked
> for me.
>
> Can anybody suggest me something. Little hint will also be helpful.
>
> Thanks a lot in advance.
>
>
> "A society with free knowledge is better than a society with free food"
>
>
> Tushar Ranjan Moharana
> B. Tech, NIT Warangal
> Ph D Student, CCMB
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