How to run a simulation with input files?

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1

GROMACS version:
GROMACS modification: Yes/No
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Hi,

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.

Many Thanks,

Amo

2

Hi Amo,

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.

3

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.

4

Hi,

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.

5

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.