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Difficulty adding the martini force field
- jcopp
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7 years 4 months ago #6570
by jcopp
Difficulty adding the martini force field was created by jcopp
Hello, I only have a few months experience with Gromacs and have only just started coarse graining.
Previously the only force field I've added to Gromacs was Charmm. However with Charmm I was able to download a folder containing all the files I needed (such as atomtypes.atp, ffbonded.itp, .rtp files ect), that I then just added to the top folder within Gromacs.
For the Martini forcefield though all I've been able to find in the download section is .itp files for particle definitions and amino acids, sugars ect. I'm wondering if I'm looking in the wrong place for these other files or if there is something I need to do to the .itp files first in order to get the force field to work?
Any help would be appreciated.
Thanks in advance.
Previously the only force field I've added to Gromacs was Charmm. However with Charmm I was able to download a folder containing all the files I needed (such as atomtypes.atp, ffbonded.itp, .rtp files ect), that I then just added to the top folder within Gromacs.
For the Martini forcefield though all I've been able to find in the download section is .itp files for particle definitions and amino acids, sugars ect. I'm wondering if I'm looking in the wrong place for these other files or if there is something I need to do to the .itp files first in order to get the force field to work?
Any help would be appreciated.
Thanks in advance.
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- peterkroon
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7 years 4 months ago #6573
by peterkroon
Replied by peterkroon on topic Difficulty adding the martini force field
Hi,
atp, rtp, hdb, ... files are used by pdb2gmx, which is unusable for coarse-grained forcefields.
Also, we don't have a list of standard bonded parameters, these have to be derived on a molecule to molecule basis anyway. So there is not ffbonded.itp.
So in your topology file, just import martini_v2.2.itp (which defines particle types and nonbonded interactions, and water), and probably you'll want to import ions as well. For the rest, mix and match as appropriate.
Peter
atp, rtp, hdb, ... files are used by pdb2gmx, which is unusable for coarse-grained forcefields.
Also, we don't have a list of standard bonded parameters, these have to be derived on a molecule to molecule basis anyway. So there is not ffbonded.itp.
So in your topology file, just import martini_v2.2.itp (which defines particle types and nonbonded interactions, and water), and probably you'll want to import ions as well. For the rest, mix and match as appropriate.
Peter
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