CHARMM36m

~ CHARMM36 force field in GROMACS format, including  CGenFF  version 4.6 and the CHARMM36m protein force field revision. Updated July 2021.

The current CHARMM36 ports for GROMACS correspond to the July 2021 toppar update. A significant addition is the presence of second set of files that include lipid parameters optimized to be used with the LJ long-range dispersion correction (ljpme, Yu et al., doi: 10.1021/acs.jctc.0c01326). Note that ljpme may be used with the remainder of the additive CHARMM force field along with the lipids. Additional changes since July 2020 include new non-standard amino acids, and extensions to CGenFF version 4.6.

The July 2021 update to the port includes the ability to use scaled water-protein interactions as was done in the CHARMM36m validation (with ε = -0.1 kcal/mol on H atoms); water-water interactions are at normal strength via the use of NBFIX. This feature is invoked by using the following keyword in the .mdp file:

charmm36-jul2021.ff.tgz

charmm36_ljpme-jul2021.ff.tgz

CHARMM  (Chemistry at HARvard Macromolecular Mechanics) is a both a set of force fields and a software package for  molecular dynamics  simulations and analysis. Includes united atom (CHARMM19) and all atom (CHARMM22, CHARMM27, CHARMM36)  force fields . The CHARMM27 force field has been ported to GROMACS and is officially supported as of version 4.5. 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.

For using CHARMM36 in GROMACS 5.0 and newer, please use the following settings in the  mdp  file:

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!

Anyone using very old versions of GROMACS may find this script useful:

CHARMM to GROMACS - perl scripts intended to facilitate calculations using GROMACS programs and CHARMM forcefields (needed for GROMACS versions < 4.5). ( link )

NA: SOD

CL: CLA

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十大健康食物排行榜 ： ·第一名 番茄
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·第十名 紫葡萄

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攸县17535884885： 阅读以下说明和C语言函数,将应填入(n)处的语句写在对应栏内.【说明...？
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