[gmx-users] Missing values in enery EDR

[Mark Abraham]

Hi,

Check your log file, where it likely says that energy groups are not
supported on GPUs. Do a rerun on your traj you want to compute these things.

Mark

On Wed, 23 Aug 2017 12:08 Sergio Manzetti <sergio.manzetti at fjordforsk.no>
wrote:

> Hi, when running gmx energy on a simulation ouput, I get:
>
> -------------------------------------------------------------------
> 1 Bond 2 Angle 3 Proper-Dih. 4 Ryckaert-Bell.
> 5 Improper-Dih. 6 LJ-14 7 Coulomb-14 8 LJ-(SR)
> 9 Disper.-corr. 10 Coulomb-(SR) 11 Coul.-recip. 12 Potential
> 13 Pres.-DC 14 Pressure 15 Vir-XX 16 Vir-XY
> 17 Vir-XZ 18 Vir-YX 19 Vir-YY 20 Vir-YZ
> 21 Vir-ZX 22 Vir-ZY 23 Vir-ZZ 24 Pres-XX
> 25 Pres-XY 26 Pres-XZ 27 Pres-YX 28 Pres-YY
> 29 Pres-YZ 30 Pres-ZX 31 Pres-ZY 32 Pres-ZZ
> 33 #Surf*SurfTen 34 T-rest
>
>
> and there are many missing values, and should be like :
>
> -------------------------------------------------------------------
> 1 Angle 2 Proper-Dih. 3 Ryckaert-Bell. 4 Improper-Dih.
> 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR)
> 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy
> 13 Conserved-En. 14 Temperature 15 Pressure 16 Constr.-rmsd
> 17 Vir-XX 18 Vir-XY 19 Vir-XZ 20 Vir-YX
> 21 Vir-YY 22 Vir-YZ 23 Vir-ZX 24 Vir-ZY
> 25 Vir-ZZ 26 Pres-XX 27 Pres-XY 28 Pres-XZ
> 29 Pres-YX 30 Pres-YY 31 Pres-YZ 32 Pres-ZX
> 33 Pres-ZY 34 Pres-ZZ
> 35 #Surf*SurfTen 36 Coul-SR:PRB-PRB
> 37 LJ-SR:PRB-PRB 38 Coul-14:PRB-PRB
> 39 LJ-14:PRB-PRB 40 Coul-SR:PRB-SOL
> 41 LJ-SR:PRB-SOL 42 Coul-14:PRB-SOL
> 43 LJ-14:PRB-SOL 44 Coul-SR:PRB-NA 45 LJ-SR:PRB-NA 46 Coul-14:PRB-NA
> 47 LJ-14:PRB-NA 48 Coul-SR:PRB-CL 49 LJ-SR:PRB-CL 50 Coul-14:PRB-CL
> 51 LJ-14:PRB-CL 52 Coul-SR:PRB-DNA
> 53 LJ-SR:PRB-DNA 54 Coul-14:PRB-DNA
> 55 LJ-14:PRB-DNA 56 Coul-SR:SOL-SOL
> 57 LJ-SR:SOL-SOL 58 Coul-14:SOL-SOL
> 59 LJ-14:SOL-SOL 60 Coul-SR:SOL-NA 61 LJ-SR:SOL-NA 62 Coul-14:SOL-NA
> 63 LJ-14:SOL-NA 64 Coul-SR:SOL-CL 65 LJ-SR:SOL-CL 66 Coul-14:SOL-CL
> 67 LJ-14:SOL-CL 68 Coul-SR:SOL-DNA
> 69 LJ-SR:SOL-DNA 70 Coul-14:SOL-DNA
> 71 LJ-14:SOL-DNA 72 Coul-SR:NA-NA 73 LJ-SR:NA-NA 74 Coul-14:NA-NA
> 75 LJ-14:NA-NA 76 Coul-SR:NA-CL 77 LJ-SR:NA-CL 78 Coul-14:NA-CL
> 79 LJ-14:NA-CL 80 Coul-SR:NA-DNA 81 LJ-SR:NA-DNA 82 Coul-14:NA-DNA
> 83 LJ-14:NA-DNA 84 Coul-SR:CL-CL 85 LJ-SR:CL-CL 86 Coul-14:CL-CL
> 87 LJ-14:CL-CL 88 Coul-SR:CL-DNA 89 LJ-SR:CL-DNA 90 Coul-14:CL-DNA
> 91 LJ-14:CL-DNA 92 Coul-SR:DNA-DNA
> 93 LJ-SR:DNA-DNA 94 Coul-14:DNA-DNA
> 95 LJ-14:DNA-DNA 96 T-System 97 Lamb-System
>
>
>
> How can I try to recoved the missing values (the sim.mdp contains all
> groups in the tcl, so everything should work)?
>
> Thanks
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>