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GROMCAS中的力场 ​

AMBER ​

AMBER（辅助建模和能量处理）既指用于模拟生物分子的一组分子机械力场，也指一套分子模拟程序。

GROMACS原生支持以下AMBER力场：

  • AMBER94
  • AMBER96
  • AMBER99
  • AMBER99SB
  • AMBER99SB-ILDN
  • AMBER03
  • AMBERGS

有关力场的信息可以使用以下信息找到：

  • AMBER Force Fields - background about the AMBER force fields
  • AMBER Programs - information about the AMBER suite of programs for molecular simulation
  • ANTECHAMBER/GAFF - Generalized Amber Force Field (GAFF) which is supposed to provide parameters suitable for small molecules that are compatible with the AMBER protein/nucleic acid force fields. It is available either together with AMBER, or through the antechamber package, which is also distributed separately. There are scripts available for converting AMBER systems (set up, for example, with GAFF) to |Gromacs| amb2gmx.pl, or ACPYPE, but they do require AmberTools_ installation to work.

CHARMM ​

CHARMM_ (Chemistry at HARvard Macromolecular Mechanics) is a both a set of force fields and a software package for :ref:molecular dynamics](gmx-md> simulations and analysis. Includes united atom (CHARMM19) and all atom (CHARMM22, CHARMM27, CHARMM36) :ref:force fields](gmx-force-field>. The CHARMM27 force field has been ported to |Gromacs| and is officially supported. CHARMM36 force field files can be obtained from the MacKerell lab website_, which regularly produces up-to-date CHARMM force field files in |Gromacs| format.

.. _CHARMM: http://www.charmm.org/ .. _MacKerell lab website: http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

For using CHARMM36 in |Gromacs|, please use the following settings in the mdp file::

constraints = h-bonds
cutoff-scheme = Verlet
vdwtype = cutoff
vdw-modifier = force-switch
rlist = 1.2
rvdw = 1.2
rvdw-switch = 1.0
coulombtype = PME
rcoulomb = 1.2
DispCorr = no

Note that dispersion correction should be applied in the case of lipid monolayers, but not bilayers.

Please also note that the switching distance is a matter of some debate in lipid bilayer simulations, and it is dependent to some extent on the nature of the lipid. Some studies have found that an 0.8-1.0 nm switch is appropriate, others argue 0.8-1.2 nm is best, and yet others stand by 1.0-1.2 nm. The user is cautioned to thoroughly investigate the force field literature for their chosen lipid(s) before beginning a simulation!

.. _gmx-gromos-ff:

GROMOS ​

.. warning:: The GROMOS force fields have been parametrized with a physically incorrect multiple-time-stepping scheme for a twin-range cut-off. When used with a single-range cut-off (or a correct Trotter multiple-time-stepping scheme), physical properties, such as the density, might differ from the intended values. Since there are researchers actively working on validating GROMOS with modern integrators we have not yet removed the GROMOS force fields, but you should be aware of these issues and check if molecules in your system are affected before proceeding. Further information is available in GitLab Issue 2884](https://gitlab.com/gromacs/gromacs/-/issues/2884>_ , and a longer explanation of our decision to remove physically incorrect algorithms can be found at DOI:10.26434/chemrxiv.11474583.v1](https://doi.org/10.26434/chemrxiv.11474583.v1>_ .

GROMOS_ is is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems. It also incorporates its own force field covering proteins, nucleotides, sugars etc. and can be applied to chemical and physical systems ranging from glasses and liquid crystals, to polymers and crystals and solutions of biomolecules.

|Gromacs| supports the GROMOS force fields, with all parameters provided in the distribution for 43a1, 43a2, 45a3, 53a5, 53a6 and 54a7. The GROMOS force fields are :ref:united atom force fields](gmx-force-field>, i.e. without explicit aliphatic (non-polar) hydrogens.

  • GROMOS 53a6 - in |Gromacs| format (J. Comput. Chem. 2004 vol. 25 (13): 1656-1676).
  • GROMOS 53a5 - in |Gromacs| format (J. Comput. Chem. 2004 vol. 25 (13): 1656-1676).
  • GROMOS 43a1p - 43a1 modified to contain SEP (phosphoserine), TPO (phosphothreonine), and PTR (phosphotyrosine) (all PO42- forms), and SEPH, TPOH, PTRH (PO4H- forms).

.. todo:: Add new force fields to the list

.. _GROMOS: https://www.igc.ethz.ch/gromos.html .. reference manual: gmx-manual-parent-dir

.. _gmx-opls:

OPLS ​

OPLS（液体模拟优化潜力）是William L.Jorgensen教授为凝聚相模拟开发的一组力场，最新版本为OPLS-AA/M。

这些力场的标准实现是由Jorgensen group小组开发的BOSS和MCPRO程序

由于没有中央网页可供参考，建议用户查阅联合原子 (OPLS-AA)和全原子 (OPLS-AA)力场的原始文献，以及Jorgensen组的页面