Hi after installation when i run,mdrun im getting an error
Can not open file:
topol.tpr
can anyone tell me what is this?
i installed in two workstations and my laptop,
first it was working in my lap,when i re install Ubuntu now in lap too this error
Regards
Nikhil
Hi,
gromacs doesn't directly work with giving just mdrun command , you will need to give it input files . Please do mdrun -h to know all the possible option for it. Also , You might need to generate tpr files for giving the input to mdrun using grompp by giving .mdp ,*.gro , *.top files. I hope that helps.
Previously when i simply giving mdrun it runs without any error,i think that is the way to check whether it working or not..
If you issue any GROMACS command without command-line options, the command will look for default file names (conf.gro, topol.tpr, etc.) The error you got means a file named "topol.tpr" does not exist in the working directory. I would recommend explicit naming of files and proper use of command-line options. Relying on defaults is very dangerous, as you can over-write files and simply lose track of what each .tpr file (and its output) was intended to do.
Thank you Justin and Vikas,
when i running for a system it works!
thanks
ROMACS: gmx mdrun, version 2016.4
Executable: /usr/local/gromacs-2016.4/bin/gmx
Data prefix: /usr/local/gromacs-2016.4
Working dir: /data/MyData/Gromacs/MethanolTutorial/Lambda_0/Production_MD
Command line:
gmx mdrun -nt 2 -deffnm md0
-------------------------------------------------------
Program: gmx mdrun, version 2016.4
Source file: src/gromacs/options/options.cpp (line 258)
Function: void gmx::Options::finish()
Error in user input:
Invalid input values
In option s
Required option was not provided, and the default file 'topol' does not
exist or is not accessible.
The following extensions were tried to complete the file name:
.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Production MD complete.
I am trying the methanol in water free energy tutorial.
This is one error I got. Question where (which directory) is the topol file supposed to be? And is it the same as the on provided in the tutorial. Can I get some help?
The error means you do not have md0.tpr in the working directory, so mdrun tries to find the default input file name (topol.tpr), which it also does not, so the run fails.
I have the topology file on my working directory, still I get the message repeatedly.
Could anyone please help me to resolve the problem?
Thanks,
Nusrat
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