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Trusted force field files for gromacs

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- aminoacids.arn
- aminoacids.c.tdb
- aminoacids.hdb
- aminoacids.n.tdb
- aminoacids.r2b
- aminoacids.rtp
- aminoacids.vsd
- atomtypes.atp
- dna.arn
- dna.hdb
- dna.r2b
- dna.rtp
- ffbonded.itp
- ffnonbonded.itp
- forcefield.doc
- forcefield.itp
- gbsa.itp
- ions.itp
- Makefile.am
- Makefile.in
- README.md
- rna.arn
- rna.hdb
- rna.r2b
- rna.rtp
- spc.itp
- spce.itp
- tip3p.itp
- tip4p.itp
- tip4pew.itp
- tip5p.itp
- urea.itp
- watermodels.dat
- - aminoacids.hdb
  - aminoacids.rtp
  - atomtypes.atp
  - ffbonded.itp
  - ffnonbonded.itp
  - README
  - residuetypes.dat
- #crw.itp.1#
- #crw.itp.2#
- aminoacids.arn
- aminoacids.c.tdb
- aminoacids.hdb
- aminoacids.n.tdb
- aminoacids.r2b
- aminoacids.rtp
- aminoacids.vsd
- atomtypes.atp
- atomtypes.atp~
- crw.itp
- cufix.itp
- dna.arn
- dna.hdb
- dna.r2b
- dna.rtp
- dna.rtp~
- ffbonded.itp
- ffbonded.itp~
- ffnonbonded.itp
- ffnonbonded.itp~
- forcefield.doc
- forcefield.doc~
- forcefield.itp
- forcefield.itp~
- gbsa.itp
- ions.itp
- Makefile.am
- Makefile.in
- rna.arn
- rna.hdb
- rna.r2b
- rna.rtp
- rna.rtp~
- spc.itp
- spce.itp
- tip3p.itp
- tip4p.itp
- tip4pew.itp
- tip5p.itp
- urea.itp
- watermodels.dat
- aminoacids.arn
- aminoacids.c.tdb
- aminoacids.hdb
- aminoacids.n.tdb
- aminoacids.r2b
- aminoacids.rtp
- aminoacids.vsd
- atomtypes.atp
- dna.arn
- dna.hdb
- dna.r2b
- dna.rtp
- ffbonded.itp
- ffnonbonded.itp
- forcefield.doc
- forcefield.itp
- gbsa.itp
- ions.itp
- Makefile.am
- Makefile.in
- README.md
- rna.arn
- rna.hdb
- rna.r2b
- rna.rtp
- spc.itp
- spce.itp
- tip3p.itp
- tip4p.itp
- tip4pew.itp
- tip5p.itp
- urea.itp
- watermodels.dat
- aminoacids.arn
- aminoacids.c.tdb
- aminoacids.hdb
- aminoacids.n.tdb
- aminoacids.r2b
- aminoacids.rtp
- aminoacids.vsd
- atomtypes.atp
- ca-sol7.itp
- ca-sol7.pdb
- cufix.itp
- dna.arn
- dna.hdb
- dna.r2b
- dna.rtp
- ffbonded.itp
- ffnonbonded.itp
- ffnonbonded.itp~
- forcefield.doc
- forcefield.itp
- forcefield.itp~
- gbsa.itp
- ions.itp
- Makefile.am
- Makefile.in
- mg-sol6.itp
- mg-sol6.pdb
- README.md
- rna.arn
- rna.hdb
- rna.r2b
- rna.rtp
- spc.itp
- spce.itp
- tip3p.itp
- tip4p.itp
- tip4pew.itp
- tip5p.itp
- urea.itp
- watermodels.dat
- - aminoacids-checkpoint.arn
  - aminoacids-checkpoint.hdb
  - aminoacids-checkpoint.r2b
  - aminoacids-checkpoint.rtp
  - aminoacids-checkpoint.vsd
  - aminoacids.c-checkpoint.tdb
  - aminoacids.n-checkpoint.tdb
  - atomtypes-checkpoint.atp
  - cufix-checkpoint.itp
  - dna-checkpoint.arn
  - dna-checkpoint.r2b
  - ffbonded-checkpoint.itp
  - ffnonbonded-checkpoint.itp
  - forcefield-checkpoint.itp
  - gbsa-checkpoint.itp
  - Makefile-checkpoint.am
  - Makefile-checkpoint.in
  - PSER-checkpoint.hdb
  - PSER-checkpoint.rtp
  - PTM-checkpoint.arn
  - residuetypes-checkpoint.dat
  - rna-checkpoint.arn
- aminoacids.arn
- aminoacids.c.tdb
- aminoacids.hdb
- aminoacids.n.tdb
- aminoacids.r2b
- aminoacids.rtp
- aminoacids.vsd
- atomtypes.atp
- ca-sol7.itp
- ca-sol7.pdb
- cufix.itp
- dna.arn
- dna.hdb
- dna.r2b
- dna.rtp
- ffbonded.itp
- ffnonbonded.itp
- ffnonbonded.itp~
- forcefield.doc
- forcefield.itp
- forcefield.itp~
- gbsa.itp
- ions.itp
- Makefile.am
- Makefile.in
- mg-sol6.itp
- mg-sol6.pdb
- PSER.hdb
- PSER.rtp
- PTM.arn
- README.md
- residuetypes.dat
- rna.arn
- rna.hdb
- rna.r2b
- rna.rtp
- spc.itp
- spce.itp
- tip3p.itp
- tip4p.itp
- tip4pew.itp
- tip5p.itp
- urea.itp
- watermodels.dat
- aminoacids.arn
- aminoacids.c.tdb
- aminoacids.hdb
- aminoacids.n.tdb
- aminoacids.r2b
- aminoacids.rtp
- aminoacids.vsd
- atomtypes.atp
- dna.arn
- dna.hdb
- dna.r2b
- dna.rtp
- ffbonded.itp
- ffnonbonded.itp
- forcefield.doc
- forcefield.itp
- frcmod.ions1lm_126_hfe_opc
- frcmod.ionsjc_tip3p
- gbsa.itp
- ions.itp
- Makefile.am
- Makefile.in
- opc.itp
- README.md
- rna.arn
- rna.hdb
- rna.r2b
- rna.rtp
- spc.itp
- spce.itp
- tip3p.itp
- tip4p.itp
- tip4pew.itp
- tip5p.itp
- urea.itp
- watermodels.dat
- - aminoacids-checkpoint.r2b
  - aminoacids-checkpoint.rtp
  - ffbonded-checkpoint.itp
  - Makefile-checkpoint.am
  - PSER-checkpoint.rtp
  - residuetypes-checkpoint.dat
- aminoacids.arn
- aminoacids.c.tdb
- aminoacids.hdb
- aminoacids.n.tdb
- aminoacids.r2b
- aminoacids.rtp
- aminoacids.vsd
- atomtypes.atp
- dna.arn
- dna.hdb
- dna.r2b
- dna.rtp
- ffbonded.itp
- ffnonbonded.itp
- forcefield.doc
- forcefield.itp
- frcmod.ions1lm_126_hfe_opc
- frcmod.ionsjc_tip3p
- gbsa.itp
- ions.itp
- Makefile.am
- Makefile.in
- opc.itp
- PSER.hdb
- PSER.rtp
- README.md
- residuetypes.dat
- rna.arn
- rna.hdb
- rna.r2b
- rna.rtp
- spc.itp
- spce.itp
- tip3p.itp
- tip4p.itp
- tip4pew.itp
- tip5p.itp
- urea.itp
- watermodels.dat
- amb2gro_top_gro_cmap.py
- build_box_prod.sh
- cpptraj_strip_solvent.in
- tleap_draft_box.rc
- aminoacids.arn
- aminoacids.c.tdb
- aminoacids.hdb
- aminoacids.n.tdb
- aminoacids.r2b
- aminoacids.rtp
- aminoacids.vsd
- atomtypes.atp
- dna.arn
- dna.hdb
- dna.r2b
- dna.rtp
- ffbonded.itp
- ffnonbonded.itp
- forcefield.doc
- forcefield.itp
- gbsa.itp
- ions.itp
- README.md
- rna.arn
- rna.hdb
- rna.r2b
- rna.rtp
- spc.itp
- spce.itp
- tip3p.itp
- tip4p.itp
- tip4pew.itp
- tip5p.itp
- urea.itp
- watermodels.dat
- - 00toppar_file_format.txt
  - par_all22_prot.prm
  - par_all35_ethers.prm
  - par_all36_carb.prm
  - par_all36_cgenff.prm
  - par_all36_lipid.prm
  - par_all36_na.prm
  - par_all36_prot.prm
  - par_all36m_prot.prm
  - par_hbond.inp
  - param19.inp
  - top_all22_prot.rtf
  - top_all35_ethers.rtf
  - top_all36_carb.rtf
  - top_all36_cgenff.rtf
  - top_all36_lipid.rtf
  - top_all36_na.rtf
  - top_all36_prot.rtf
  - toph19.inp
  - toppar_all.history
  - toppar_water_ions.str
- atomtypes.atp
- cmap.itp
- ffbonded.itp
- ffnonbonded.itp
- forcefield.doc
- forcefield.itp
- gb.itp
- ions.itp
- merged.arn
- merged.c.tdb
- merged.hdb
- merged.n.tdb
- merged.r2b
- merged.rtp
- merged.vsd
- nbfix.itp
- old_c36_cmap.itp
- README.md
- spc.itp
- spce.itp
- tip3p.itp
- tip4p.itp
- watermodels.dat
- - 00toppar_file_format.txt
  - par_all22_prot.prm
  - par_all35_ethers.prm
  - par_all36_carb.prm
  - par_all36_cgenff.prm
  - par_all36_lipid.prm
  - par_all36_na.prm
  - par_all36_prot.prm
  - par_all36m_prot.prm
  - par_hbond.inp
  - param19.inp
  - top_all22_prot.rtf
  - top_all35_ethers.rtf
  - top_all36_carb.rtf
  - top_all36_cgenff.rtf
  - top_all36_lipid.rtf
  - top_all36_na.rtf
  - top_all36_prot.rtf
  - toph19.inp
  - toppar_all.history
  - toppar_water_ions.str
- atomtypes.atp
- cmap.itp
- convert_cufix.py
- ffbonded.itp
- ffnonbonded.itp
- forcefield.doc
- forcefield.itp
- gb.itp
- ions.itp
- merged.arn
- merged.c.tdb
- merged.hdb
- merged.n.tdb
- merged.r2b
- merged.rtp
- merged.vsd
- nbfix.itp
- old_c36_cmap.itp
- README.md
- spc.itp
- spce.itp
- tip3p.itp
- tip4p.itp
- toppar_water_ions_cufix.str
- toppar_water_ions_cufix_simpl.str
- watermodels.dat
- frcmod.ionsjc_tip3p
.gitignore
README.md

// repository documentation

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# gromacs_ff
Trusted force field files for gromacs in this repo:

- https://github.com/intbio/gromacs_ff/tree/master/amber14sb_parmbsc1.ff AMBER ff with parmbsc1 corrections to simulate DNA from Gromacs web-site
- https://github.com/intbio/gromacs_ff/tree/master/amber14sb_parmbsc1_cufix.ff same ff but with CUFIX corrections
- https://github.com/intbio/gromacs_ff/tree/master/amber14sb_OL15.ff AMBER ff with OL15 refinements to simulate DNA (this is an alternative to pambsc1 as of Amber19) from Gromacs web-site
- https://github.com/intbio/gromacs_ff/tree/master/amber14sb_parmbsc1_opc_lmi.ff - this is the corresponding AMBER ff but with OPC water model and Li/Merz ions implemented by @molsim - testing is still needed
- https://github.com/intbio/gromacs_ff/tree/master/charmm36-mar2019.ff CHARMM36/36m force field from [MacKerrel Lab](http://mackerell.umaryland.edu/charmm_ff.shtml)
- https://github.com/intbio/gromacs_ff/tree/master/charmm36-mar2019_cufix.ff CHARMM36/36m ff with CUFIX corrections implemented by @molsim - testing is still needed.

## General notes on available force fields
### Simulating DNA
- The best source of information is usually the Amber manual. Currently, [Amber 19 manual](http://ambermd.org/doc12/Amber19.pdf) on page 38 discusses two options parmbsc1 from Orozco group and OL15 from Sponer group. The do not make a choice as to which is better, howerver, on the front page the OL15 is recommended.
- As for ions, by default the Young Cheatham 2008 ions are selected in Amber ff. Looks like it may be a good idea to replace them with CUFIX from Aksimentiev group.
- The amber14sb_parmbsc1_cufix is available in this repo.
- The amber OL15 can be downloaded from the gromacs web-site.

### Simulating disordered proteins
- There is CHARMM36m (2016) ff, it is now recommended for all protein simulations, can be found at MacKerells web-page (see below). Also ports for Gromacs are there.
- In AMBER another way is to use OPC water model (see this paper https://pubs.acs.org/doi/10.1021/acs.jctc.8b01123) with 12-6 HFE Li and Merz ion parameters. We need to add a gromacs prot here ...

### Simulations of proteins and protein folding
- Generally there are two options standard latest AMBER or CHARMM force fields.
- See AMBER manual for AMBER, currently the ff14SB is recommended.
- See MacKerell web-site for CHARMM http://mackerell.umaryland.edu/charmm_ff.shtml . Strictly speaking the charmm ff is updated with each new release of charmm (currently 44). However, since CHARMM36 the changes have been small, so on MacKerell's web-page they are reffered as updates to the CHARMM36 ff.

## Links to external ff resources
### AMBER
- http://ambermd.org/AmberModels.php
- http://ambermd.org/doc12/Amber18.pdf see section 3.
- As of 2018 -  ff14SB is the recommended protein force field in Amber.
- ff14SB paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4821407/pdf/nihms772276.pdf
- For DNA one should use currently  PARMBSC1 corrections with AMBER or OL15.
- Ion parameters are important see [section 3.6](http://ambermd.org/doc12/Amber18.pdf). Amber currently recommends Li & Merz parameters (2015).
- [CUFIX corrections](http://bionano.physics.illinois.edu/CUFIX) by Yoo & Aksimentiev, 2018, are important for charged systems
- [OL ff refinements for DNA and RNA](https://fch.upol.cz/ff_ol/index.php)
- [OPC water model](https://bioinformatics.cs.vt.edu/~izadi/)

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