Dear All,
I am trying to run US in gromacs for my protein-lipid system in version 5.0.2.
I tried to simulate the same system using the attached pull.mdp file in Gromacs 4.6.x. It was running fine.
Now I have upgraded my gromacs to 5.0.2. It is giving many warnings followed by a fatal error.
WARNING 1 [file pull.mdp, line 70]:
Unknown left-hand 'pull_ngroups' in parameter file
WARNING 2 [file pull.mdp, line 70]:
Unknown left-hand 'pull_ncoords' in parameter file
(12 similar warnings followed by fatal error for all pull code parameters).
Could somebody please check the attached pull.mdp file and suggest how to modify it. I also have tried the tutorial pull.mdp file at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/md_pull.mdp. But, I am getting the same error for my system.
Thanking you in anticipation
Best regards
Bikash
James is right.
Gromacs 5.1 provides more flexibility in defining the reaction pull parameters, so you should ideally install the latest code.
But, in case you don't have access to administrative rights or for some reason can't upgrade, the easiest way is to use the copy of mdp file which gromacs saves as mdout.mdp. Whenever you run mdrun, it saves a copy of the parameter file (compatible with the current version) in the same folder where you have your pull.mdp file. Now, you can edit this new copy to provide you run parameters and use it as your parameter input file with mdrun.
Hope this helps. Happy simulating.
Thank you Dr. James and Acharya.
I will try to upgrade the Gromacs.
I am little worried if really the mdout.mdp will work. But it seems interesting. I will try for sure.
Best regards
Bikash
i am also getting the same problem for protein ligand complex. please tell me how to fix if its is possible please send me md_pull.mdp file for gromacs 4.6.
Mr James “Wes” Barnett, i can't upgrade 4.5.4, what should i do now?
please help me
thank you so much
hello
i am using version 5.0.4, and i am still getting all errors with md_pull.mdp.
Please someone help me with this.
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