Dear all,
I am setting up a simulation with mixed solvent using the gromos54a8 force field. I have followed the procedure described in the Gromacs how-to for mixed solvent and several answers in the Gromacs forum.
I have seen that most solvents (such as TFE, CCl4, CH3OH, etc) are in the aminoacids.rtp file and not as separate itp files. Therefore, I cannot include them in topol.top and I cannot define my co-solvent (TFE) as a separate molecule in [ molecules ] section. Should I create an itp file from the aminoacids.rtp or is there a cleaner way to do the setup?
Thanks,
Ramon
I believe they’re all in the single rtp file due to how the conversion of the GROMOS software
formatted force field files have been automatically converted into GROMACS format.
To make an itp from the rtp then it is probably easiest to generate the structure of a single molecule and use pdb2gmx to generate the topology (.top) from which you just need to remove a few lines to make the itp.
Thanks Tom,
That was very useful.
As I am using Gromos I also read carefully the discussion in this thread I wanted to ask you if the your work testing different setups has been published. I could not find it and it would be very helpful to the community.