Unknown

Dataset Information

0

Optimizing Solute-Solute Interactions in the GLYCAM06 and CHARMM36 Carbohydrate Force Fields Using Osmotic Pressure Measurements.

ABSTRACT: GLYCAM06 and CHARMM36 are successful force fields for modeling carbohydrates. To correct recently identified deficiencies with both force fields, we adjusted intersolute nonbonded parameters to reproduce the experimental osmotic coefficient of glucose at 1 M. The modified parameters improve behavior of glucose and sucrose up to 4 M and improve modeling of a dextran 55-mer. While the modified parameters may not be applicable to all carbohydrates, they highlight the use of osmotic simulations to optimize force fields.

SUBMITTER: Lay WK 

PROVIDER: S-EPMC5082696 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature

Json Xml
altmetric image

Publications

Optimizing Solute-Solute Interactions in the GLYCAM06 and CHARMM36 Carbohydrate Force Fields Using Osmotic Pressure Measurements.

Lay Wesley K WK   Miller Mark S MS   Elcock Adrian H AH  

Journal of chemical theory and computation 20160322 4

GLYCAM06 and CHARMM36 are successful force fields for modeling carbohydrates. To correct recently identified deficiencies with both force fields, we adjusted intersolute nonbonded parameters to reproduce the experimental osmotic coefficient of glucose at 1 M. The modified parameters improve behavior of glucose and sucrose up to 4 M and improve modeling of a dextran 55-mer. While the modified parameters may not be applicable to all carbohydrates, they highlight the use of osmotic simulations to o  ...[more]

Similar Datasets

Unknown Carbohydrate force fields.
| S-EPMC4270206 | biostudies-literature
Unknown Reparameterization of Solute-Solute Interactions for Amino Acid-Sugar Systems Using Isopiestic Osmotic Pressure Molecular Dynamics Simulations.
| S-EPMC5844349 | biostudies-literature
Unknown Reparametrization of Protein Force Field Nonbonded Interactions Guided by Osmotic Coefficient Measurements from Molecular Dynamics Simulations.
| S-EPMC5543770 | biostudies-literature
Unknown Cation-π Interactions between Methylated Ammonium Groups and Tryptophan in the CHARMM36 Additive Force Field.
| S-EPMC6467778 | biostudies-literature
Unknown Osmotic Engine: Translating Osmotic Pressure into Macroscopic Mechanical Force via Poly(Acrylic Acid) Based Hydrogels.
| S-EPMC5604390 | biostudies-literature
Unknown Evaluating and optimizing computational protein design force fields using fixed composition-based negative design.
| S-EPMC2516967 | biostudies-literature
Unknown Under pressure: force resistance measurements in box mites (Actinotrichida, Oribatida).
| S-EPMC6611053 | biostudies-literature
Unknown Proper balance of solvent-solute and solute-solute interactions in the treatment of the diffusion of glucose using the Drude polarizable force field.
| S-EPMC5809005 | biostudies-literature
Unknown Competition among Li(+), Na(+), K(+), and Rb(+) monovalent ions for DNA in molecular dynamics simulations using the additive CHARMM36 and Drude polarizable force fields.
| S-EPMC4378841 | biostudies-literature
Unknown Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements.
| S-EPMC3383641 | biostudies-literature