GROMACS modification: Yes/No
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I have downloaded the necessary files (equilibration.inp and production.inp files) to carry out a simulation on Gromacs from the Multicomponent Assembler in Charmm in the form of the tgz. file and this was extracted. However, in order to run the simulation, I believe the files need to be in an mdp format?
The Job Retriever ID is: 9621133563
I would appreciate any advice on on how to proceed with the simulation on Ubuntu using the files obtained.
It seems like you received a charmm input file, GROMACS uses no .inp files, but instead files like .top and .itp for molecule topologies and .gro, .pdb for structures and .mdp for simulation parameter settings.
Unfortuntately I don’t have much experience with converting CHARMM parameters to GROMACS, other form users or google might help you further here.
Hi. I used CHARMM-GUI before. It had provided all of the input files that I wanted in “gromacs folder”! Maybe it’s better to regenerate your structure seperatly for GROMACS and AMMBER and choose forcefields which are suitable for each programm.
Thank you for your reply. I would like to carry out a simulation of Insulin against a silica surface, but would that not require them to be together?
Also, in CHARMM-GUI, I selected to receive my files as in Gromacs format but I get an error - ‘ISC4’.
If I follow your proposed method to regenerate my structure then what input generator would I utilise on CHARMM-GUI?
I would appreciate any advice as I am newbie to this program and currently stuck and cannot report back to my colleague for advice as they are out of office.
Maybe it’s better to direct this problem to charmm-gui providers.
I’m not experienced enough in simulation as well, I used charmm-gui to generate complex micelle-protein, but as it mentioned in charmm-gui for modeling Silica: bulk minerals (α-quartz, α-cristobalite) as well as surfaces of different degree of ionization for specific pH values and particle sizes, you can use Nanomaterial Modeler.