GROMACS version:
GROMACS modification: Yes/No
Dear Justin,
Charmm-gui provided me with a series of mdp files for a membrane, but the parameters in those files are different from your tutorial. Are the mdp files generated by Charmm-gui valid and good enough to do an MD simulation? Can I use these mdp files? For example, there isn’t PBC option in these files.
Can I expand the nsteps option in these files and do a simulation? Is it correct?
Thanks
The .mdp files that CHARMM-GUI provides are appropriate. I’m not going to comment on individual keywords or small differences without more context and actual details.
Thank you, dear Justin.
I tried to build a bilayer-protein system using charm-gui. I ticked to gromacs input at step 6. However, charm-gui did not give gromacs input files like .mdp files. It was giving files such as .inp several times when I tried. Is this a bug? I clearly ticked Gromacs. Forcefield was CHARMM36
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If you’re having problems with CHARMM-GUI, reach out to their developers. But I have never seen an issue in which inputs were requested and not generated at this phase. Use the Job Retriever to revisit the final step and try to generate the GROMACS inputs again.
Did you ever reach out or find a solution? This is also happening to me.
Again I would emphasize that this is not a GROMACS problem and therefore not solvable on this forum. If you have an issue with CHARMM-GUI, their developers will need to address it.
Hi,
I had mistakenly reported that there were no Gromacs input files. I looked only at the output bar of the Charm-gui web interface at the final step. In that there were no Gromacs output files were reported as output. However, there were Gromacs files in the zipped output file I downloaded at the final step. Surely, you can find the Gromacs input files in the Zipped folder if you correctly tick the Gromacs option at the particular step.
Sorry for my mistake!
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hi @dr_m_ganj I am using CHARMM-GUI generated files during my undergraduate research. As an inexperienced student, CHARMM-GUI was still very helpful to me. However, I think an experienced researcher could change those parameters appropriately. Also, I think PBC are considered by default by GROMACS even if the PBC option is not in the MDP file. I have seen that researchers have used CHARMM-GUI-generated files in several publications found in the literature, with or without modifications.