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标题: 蒙脱石-离子溶液-冰晶三相能量极小化不收敛 [打印本页]

作者
Author: TCN 时间: 前天 15:04
标题: 蒙脱石-离子溶液-冰晶三相能量极小化不收敛
蒙脱石-离子溶液-冰晶三相能量极小化不收敛；三相体系中蒙脱石单胞、水分子、和冰晶的单胞均未作DFT优化，采用packmol建模后直接进行能量极小化结果不收敛，蒙脱石采用Clayff力场，水和冰采用tip4p-ice力场，附件是em.mdp、em.log、em.gro。以上不收敛问题该如何排查

作者
Author: sobereva 时间: 前天 16:15
明明已经收敛了

Polak-Ribiere Conjugate Gradients converged to Fmax < 1000 in 44 steps
Potential Energy  = -2.4377318e+06
Maximum force    =  8.4311212e+02 on atom 746
Norm of force    =  4.6245891e+01

作者
Author: 牧生 时间: 前天 18:28
vmd打开你的em.gro，有很多

Warning) Unusual bond between residues:  11 (none) and 117 (waters)
Warning) Unusual bond between residues:  11 (none) and 117 (waters)
Warning) Unusual bond between residues:  13 (none) and 596 (waters)
Warning) Unusual bond between residues:  13 (none) and 596 (waters)
Warning) Unusual bond between residues:  15 (none) and 570 (waters)
Warning) Unusual bond between residues:  15 (none) and 570 (waters)
Warning) Unusual bond between residues:  16 (none) and 1025 (waters)
Warning) Unusual bond between residues:  16 (none) and 1025 (waters)
Warning) Unusual bond between residues:  17 (none) and 42 (waters)
Warning) Unusual bond between residues:  17 (none) and 42 (waters)
Warning) Unusual bond between residues:  18 (none) and 871 (waters)
Warning) Unusual bond between residues:  18 (none) and 871 (waters)

说明你的拓扑文件，或者顺序不对

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