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标题: 液液萃取时遇到待萃物无法进入萃取剂该如何解决 [打印本页]

作者
Author: chansens 时间: 2025-2-25 16:32
标题: 液液萃取时遇到待萃物无法进入萃取剂该如何解决
tolerance 2.0
filetype pdb
output extraction.pdb
add_box_sides

structure H2O.pdb
  number 18255
  inside box 0. 0. 50. 100. 100. 150.
end structure

structure N8881+.pdb
  number 192
  inside box 0. 0. 0. 100. 100. 50.
end structure

structure N8881+.pdb
  number 192
  inside box 0. 0. 150. 100. 100. 200.
end structure

structure Br-.pdb
  number 192
  inside box 0. 0. 0. 100. 100. 50.
end structure

structure Br-.pdb
  number 192
  inside box 0. 0. 150. 100. 100. 200.
end structure

structure DA.pdb
  number 384
  inside box 0. 0. 0. 100. 100. 50.
end structure

structure DA.pdb
  number 384
  inside box 0. 0. 150. 100. 100. 200.
end structure

structure PC.pdb
  number 150
  inside box 0. 0. 0. 100. 100. 50.
end structure

structure PC.pdb
  number 150
  inside box 0. 0. 150. 100. 100. 200.
end structure

我的盒子两端放的低共熔溶剂，中间部分是水，考虑到低共熔粘度较大，md.mdp文件里已经把温度升高到80了，结果还是不理想，与实验对不上，请问是否可以加一点扰动试试呢？

作者
Author: sobereva 时间: 2025-2-26 12:24
建模的时候就把待萃物放到萃取剂里，看看动力学过程中待萃取物会不会跑出去，如果这样，说明力场参数或原子电荷本身就有问题。至于你说引入扰动，可以做拉伸动力学把待萃物拉进去

作者
Author: chansens 时间: 2025-3-3 10:26

sobereva 发表于 2025-2-26 12:24
建模的时候就把待萃物放到萃取剂里，看看动力学过程中待萃取物会不会跑出去，如果这样，说明力场参数或原子 ...

谢谢老师，我使用Gaussian在B3LYP(BJ)/Def2-TZVP级别下计算得到RESP2(0.5)电荷后，使用Sobtop软件生成适用于GROMACS使用的top文件

#include "amber14sb/forcefield.itp"
#include "amber14sb/spce.itp"
#include "H2O.itp"
#include "N8881+.itp"
#include "Br-.itp"
#include "DA.itp"

[ system ]
extraction

[ molecules ]
; Compound       nmols
H2O       20984
N8881+    443
Br-    443
DA       886

; Created by Sobtop (http://sobereva.com/soft/sobtop) Version 1.0(dev3.1) on 2024-07-29

[ atomtypes ]
; name at.num    mass    charge ptype    sigma (nm) epsilon (kJ/mol)
oh          8 15.999405 0.000000 A    3.066473E-01 8.803136E-01
ho          1    1.007941 0.000000 A    0.000000E+00 0.000000E+00

[ atomtypes ]
; name at.num    mass    charge ptype    sigma (nm) epsilon (kJ/mol)
c3          6 12.010736 0.000000 A    3.399670E-01 4.577296E-01
hx          1    1.007941 0.000000 A    1.959977E-01 6.568880E-02
hc          1    1.007941 0.000000 A    2.649533E-01 6.568880E-02
n4          7 14.006703 0.000000 A    3.249999E-01 7.112800E-01

[ atomtypes ]
; name at.num    mass    charge ptype    sigma (nm) epsilon (kJ/mol)
br       35 79.903528 0.000000 A    3.599231E-01 1.757280E+00

[ atomtypes ]
; name at.num    mass    charge ptype    sigma (nm) epsilon (kJ/mol)
c31          6 12.010736 0.000000 A    3.399670E-01 4.577296E-01
hc1          1    1.007941 0.000000 A    2.649533E-01 6.568880E-02
h1          1    1.007941 0.000000 A    2.471353E-01 6.568880E-02
oh1          8 15.999405 0.000000 A    3.066473E-01 8.803136E-01
ho1          1    1.007941 0.000000 A    0.000000E+00 0.000000E+00

[ atomtypes ]
; name at.num    mass    charge ptype    sigma (nm) epsilon (kJ/mol)
c32          6 12.010736 0.000000 A    3.399670E-01 4.577296E-01
c          6 12.010736 0.000000 A    3.399670E-01 3.598240E-01
h11          1    1.007941 0.000000 A    2.471353E-01 6.568880E-02
os          8 15.999405 0.000000 A    3.000012E-01 7.112800E-01
o          8 15.999405 0.000000 A    2.959922E-01 8.786400E-01
hc2          1    1.007941 0.000000 A    2.649533E-01 6.568880E-02

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