[gmx-users] Probable bug in 5.0.4 gmx enemat

[Mark Abraham]

Hi,

You can try a 4.6 version where you think the earlier bug is fixed, on the
5.0. edr, to see if it is the same.

On Fri, 14 Aug 2015 17:32 Tushar Ranjan Moharana <
tusharranjanmoharana at gmail.com> wrote:

> Hi friends,
> I want to analyze interaction energy between 2 groups of atoms. I use gmx
> enemat. However I got following errors.
>
> Opened FOA2_lip_pull.edr as single precision energy file
> Will read groupnames from inputfile
> Read 2 groups
> group 0WARNING! could not find group Coul-SR:Protein-Protein (0,0)in energy
> file
> WARNING! could not find group LJ-SR:Protein-Protein (0,0)in energy file
> WARNING! could not find group Coul-SR:Protein-Non-protein (0,1)in energy
> file
> WARNING! could not find group LJ-SR:Protein-Non-protein (0,1)in energy file
> group 1WARNING! could not find group Coul-SR:Non-protein-Non-protein
> (1,1)in energy file
> WARNING! could not find group LJ-SR:Non-protein-Non-protein (1,1)in energy
> file
>
> Will select half-matrix of energies with 0 elements
> Last energy frame read 1400 time 1400.000
> Will build energy half-matrix of 2 groups, 0 elements, over 1401 frames
> Segmentation fault (core dumped)
>
> I am using gromacs5.0.4 version (Quick and dirty installation). In
> gromacs4.6 there was bug which used to cause similar problem but latter it
> got fixed. I want to know whether it is another bug? What is the solution
> for that?
>
> My command line was    gmx enemat -f FOA2_lip_pull.edr  -groups
> energy_groups.dat -etot FOA1_lip_push_en.xvg -mean -temp 310
>
> I tried many other combination which includes changing energy_groups.dat
> content, analyzing a different .edr file and removing -mean and -temp flags
> etc.
>
> Please help me to solve this. Thanks for your time and effort.
>
>
>
>
> "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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