[gmx-users] calculating energy between certain groups

[Tasneem Kausar]

First of all define energy groups in mdp file. Then run gmx grompp with
that mdp to generate a new tpr. In gmx mdrun provide reference file (eg
tpr).


On Mon, May 21, 2018 at 7:19 AM, Irem Altan <irem.altan at duke.edu> wrote:

> I tried the following:
>
> mdrun -rerun umbrella0.xtc -np cpu -deffnm umbrella0
>
> and also I can verify from the output file that it didn’t use GPUs.
> However, I still get the same error with gmx enemat:
>
> GROMACS:      gmx enemat, version 2016.3
> Executable:   /opt/gromacs/bin/gmx_mpi
> Data prefix:  /opt/gromacs
> Working dir:  /oasis/scratch/comet/nano3/temp_project/c4_m_4C/rerun
> Command line:
>   gmx_mpi enemat -f umbrella0.edr
>
> Opened umbrella0.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-SOL (0,1)in energy file
> WARNING! could not find group LJ-SR:Protein-SOL (0,1)in energy file
> group 1WARNING! could not find group Coul-SR:SOL-SOL (1,1)in energy file
> WARNING! could not find group LJ-SR:SOL-SOL (1,1)in energy file
>
> Will select half-matrix of energies with 0 elements
> Last energy frame read 2000 time 20000.000
> Will build energy half-matrix of 2 groups, 0 elements, over 2001 frames
> Segmentation fault
>
> What could be the problem?
>
> Best,
> Irem
> --
> 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.