本例使用moltemplate通过定制force field的lt文件和一个python脚本可批量生成任意聚合度的全氟聚醚data文件。该方法采用的OPLSAA力场参数来自文献Perfluoropolyethers: Development of an All-Atom Force Field forMolecular Simulations and Validation with New Experimental VaporPressures and Liquid Densities。这里采用的...
1998 Development of the OPLS-AA force field for organic and biomolecular systems. Abstr. Pap. Am. Chem. Soc. 216, U696.W. L. Jorgensen and J. Tirado-Rives, "Development of the OPLS-AA force field for organic and biomolecular systems.," Abstr Pap Am Chem S Abstr Pap Am Chem S, ...
OPLS-AA force field parameters have been developed and validated for use in the simulation of 68 unique combinations of room temperature ionic liquids featuring 1-alkyl-3-methylimidazolium [RMIM] (R = Me, Et, Bu, Hex, Oct), N-alkylpyridinium [RPyr], and choline cations, along with Cl(-...
If you want to use pdb2gmx to automatically generate your topology, you have toensure that the appropriate .rtp entry is present within the desired force fieldand has the same name as the building block you are trying to use (again, thisis spelled out in Chapter 5 of the manual). If ...
Why the OPLS-AA force field cannot produce the beta-hairpin structure of H1 peptide in solution when comparing with the GROMOS 43A1 force field? Why the OPLS-AA force field cannot produce the beta-hairpin structure of H1 peptide in solution when comparing with the GROMOS 43A1 force field?
A lazy script to calculate 1.2*CM5 atomic charges suitable for OPLS-AA force field simulation ...
A lazy script to calculate 1.2*CM5 atomic charges suitable for OPLS-AA force field simulation 文/Sobereva@北京科音2021-Jan-28 根据J. Phys. Chem. B., 121, 3864 (2017)中的测试,基于OPLS-AA力场的模拟很适合结合1.2*CM5原子电荷。虽然用1.2*CM5的时候水合自由能的计算精度稍逊于文中测试的另一种原...
We then optimized the current OPLS-AA force field. MD simulations of several globular proteins using new OPLS-AA/C force field give significantly less deviation (RMSD) to PDB structures than using the OPLS-AA/L. Our new force field not only better reproduces the experiments of short unfolded...
jiaoyixiong (站内联系TA)你得看看你自己所使用的gromacs版本吧？你打一个 pdb2gmx 回车就可以看到：比如我的版本：Select the Force Field:From '/share/gromacs/top':1: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)2: AMBER94 force field (Cornell et al...
István, K, Michael, CO, Richard, FM, Sandor, L (2008) Development of glycyl radical parameters for the OPLS-AA/L force field. Journal of Computational Chemistry 29: pp. 1999-2009István K, et al. J Comput Chem. 2008; 29 :1999.Istvan, K., Michael, C. O., Richard, F. M., &...