Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: Influence on the folding properties of two beta-peptides in methanol

2012 ◽  
Vol 33 (24) ◽  
pp. 1907-1917 ◽  
Author(s):  
Bruno A. C. Horta ◽  
Zhixiong Lin ◽  
Wei Huang ◽  
Sereina Riniker ◽  
Wilfred F. van Gunsteren ◽  
...  
Keyword(s):  
Force Field ◽  
Model Compound ◽  
Interaction Parameters ◽  
Peptide Backbone ◽  
Beta Peptides ◽  
Gromos Force Field ◽  
Field Influence

New Interaction Parameters for Charged Amino Acid Side Chains in the GROMOS Force Field

2012 ◽  
Vol 8 (10) ◽  
pp. 3705-3723 ◽  
Author(s):  
Maria M. Reif ◽  
Philippe H. Hünenberger ◽  
Chris Oostenbrink
Keyword(s):  
Amino Acid ◽  
Force Field ◽  
Interaction Parameters ◽  
Side Chains ◽  
Amino Acid Side Chains ◽  
Gromos Force Field

scholarly journals Methylguanidinium at the Air/Water Interface: A Simulation Study with the Drude Polarizable Force Field

2020 ◽  
Author(s):  
Jian Zhu ◽  
Jing Huang
Keyword(s):  
Force Field ◽  
Model Compound ◽  
Side Chain ◽  
Water Interface ◽  
Polarizable Force Field ◽  
Polarization Effects ◽  
Structure And Dynamics ◽  
Arginine Side Chain ◽  
Air Water Interface ◽  
Dynamics Simulations

<div>Methylguanidinium is an important molecular ion which also serves as the model compound for arginine side chain. We studied the structure and dynamics of methylguanidium ion at the air/water interface by molecular dynamics simulations employing the Drude polarizable force field. We found out that methylguanidinium accumulate on the interface with a majority adopting tilted conformations. We also demonstrated that methylguanidinium and guanidinium ions have different preference towards the air/water interface. Our results illustrate the importance to explicitly include the electronic polarization effects in modeling interfacial properties.</div><div><br> </div>

scholarly journals Definition and testing of the GROMOS force-field versions 54A7 and 54B7

2011 ◽  
Vol 40 (7) ◽  
pp. 843-856 ◽  
Author(s):  
Nathan Schmid ◽  
Andreas P. Eichenberger ◽  
Alexandra Choutko ◽  
Sereina Riniker ◽  
Moritz Winger ◽  
...  
Keyword(s):  
Force Field ◽  
Gromos Force Field
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