[gmx-users] Probable bug in 5.0.4 gmx enemat

[Mark Abraham]

Hi,

So you've concluded that there's no implementation of gmx enemat that ever
worked for your use case? What command line is that?

Mark

On Fri, Aug 21, 2015 at 5:13 PM Tushar Ranjan Moharana <
tusharranjanmoharana at gmail.com> wrote:

> Hi Mark,
> As per your suggestion I have tried 4.6.7 version and also installed
> gromacs in debug mode. However that didn't help. I got the same error as
> follows;
>
>
>
>
>
>
>
>
>
> *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)*
>
> When I use g_energy I was prompt to choose which energy I want as shown
> below
>
> 2505  LJ-SR:MET24-THR177                 2506
> Coul-14:MET24-THR177
> 2507  LJ-14:MET24-THR177                 2508
> Coul-SR:MET24-ASP178
> 2509  LJ-SR:MET24-ASP178                 2510
> Coul-14:MET24-ASP178
> 2511  LJ-14:MET24-ASP178                 2512
> Coul-SR:MET24-GLN184
> 2513  LJ-SR:MET24-GLN184                 2514
> Coul-14:MET24-GLN184
> 2515  LJ-14:MET24-GLN184                 2516
> Coul-SR:MET24-ALA190
> 2517  LJ-SR:MET24-ALA190                 2518
> Coul-14:MET24-ALA190
> 2519  LJ-14:MET24-ALA190                 2520
> Coul-SR:MET24-ALA191
> 2521  LJ-SR:MET24-ALA191                 2522
> Coul-14:MET24-ALA191
> 2523  LJ-14:MET24-ALA191                 2524  Coul-SR:MET24-ALA194
>
> and when I choose a number and 0 it shows
>
>
>
>
>
>
>
> *Statistics over 1000001 steps [ 0.0000 through 2000.0000 ps ], 1 data
> setsAll statistics are over 10001 pointsEnergy
> Average   Err.Est.       RMSD
>
> Tot-Drift-------------------------------------------------------------------------------LJ-SR:LEU244-ODA
> -0.150913       0.11    0.43633   0.017812  (kJ/mol)*
>
> Which seems to be correct. But then my question is why gmx enemat is giving
> error and what is the solution for that. I want to calculate the average
> non-bonded energy between various energy groups. gmx energy is giving me a
> particular energy between 2 group as a function of time.
>
> 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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