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Hi I need to get the latest gro file using xtc .I used below ;
I get a notification as error in input file.Please advice
srun --cpu-bind=cores --gpu-bind= none --module cuda-mpich shifter gmx_mpi mdrun trjconv -f PSS25PEPgpu30.xtc -s nvt30.tpr -o NewgroPSS25PEPgpu30.xtc
:-) GROMACS - gmx mdrun, 2023.2-dev-20230712-a3d6917ec9-dirty-unknown (-:
Executable: /opt/gromacs/install/bin/gmx_mpi
Data prefix: /opt/gromacs/install
Working dir: /pscratch/sd/r/rsivara/Backupperlmutter202495by105/DiblockPS-PEP/Trial3/PSSF25-6K-PEP15K/Perlmuttercpuruns/Longbonddeletion/Palmettoruns/Lon gbonddeletioncutoff2/Palmettoruns/Sodiumrenumber/Longbondscheck/DrGrestruns/GROMACSRUNS/Grorune30-1/Clusteranalysis
Command line:
gmx_mpi mdrun trjconv -f PSS25PEPgpu30.xtc -s nvt30.tpr -o NewgroPSS25PEPgpu30.xtc
Program: gmx mdrun, version 2023.2-dev-20230712-a3d6917ec9-dirty-unknown
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 167)
Function: void gmx::CommandLineParser::parse(int*, char**)
MPI rank: 0 (out of 4)
Error in user input:
Positional argument 'trjconv' cannot be accepted. Perhaps you forgot to put a
hyphen before an option name.
Hi I need to get the latest gro file using xtc .I used below ;
I get a notification as error in input file.Please advice
srun --cpu-bind=cores --gpu-bind= none --module cuda-mpich shifter gmx_mpi mdrun trjconv -f PSS25PEPgpu30.xtc -s nvt30.tpr -o NewgroPSS25PEPgpu30.xtc
:-) GROMACS - gmx mdrun, 2023.2-dev-20230712-a3d6917ec9-dirty-unknown (-:
Executable: /opt/gromacs/install/bin/gmx_mpi
Data prefix: /opt/gromacs/install
Working dir: /pscratch/sd/r/rsivara/Backupperlmutter202495by105/DiblockPS-PEP/Trial3/PSSF25-6K-PEP15K/Perlmuttercpuruns/Longbonddeletion/Palmettoruns/Lon gbonddeletioncutoff2/Palmettoruns/Sodiumrenumber/Longbondscheck/DrGrestruns/GROMACSRUNS/Grorune30-1/Clusteranalysis
Command line:
gmx_mpi mdrun trjconv -f PSS25PEPgpu30.xtc -s nvt30.tpr -o NewgroPSS25PEPgpu30.xtc
Program: gmx mdrun, version 2023.2-dev-20230712-a3d6917ec9-dirty-unknown
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 167)
Function: void gmx::CommandLineParser::parse(int*, char**)
MPI rank: 0 (out of 4)
Error in user input:
Positional argument 'trjconv' cannot be accepted. Perhaps you forgot to put a
hyphen before an option name.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Program: gmx mdrun, version 2023.2-dev-20230712-a3d6917ec9-dirty-unknown
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 167)
Function: void gmx::CommandLineParser::parse(int*, char**)
MPI rank: 3 (out of 4)
Error in user input:
Positional argument 'trjconv' cannot be accepted. Perhaps you forgot to put a
hyphen before an option name.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Program: gmx mdrun, version 2023.2-dev-20230712-a3d6917ec9-dirty-unknown
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 167)
Function: void gmx::CommandLineParser::parse(int*, char**)
MPI rank: 2 (out of 4)
Error in user input:
Positional argument 'trjconv' cannot be accepted. Perhaps you forgot to put a
hyphen before an option name.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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