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本帖最后由 FrancisCho 于 2024-6-13 19:21 编辑
GMX的mdp指令中如何实现对一个原子/组施加一个力，使其穿过碳纳米管？
我在复刻完GMX官方的Umbrella Sampling教程（http://www.mdtutorials.com/gmx/umbrella/05_pull.html）后想将其迁移至自己研究的体系中。
针对教程中给的相关文件，我对其进行修改，在md_pull.mdp中使用如下指令：
; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = NA
pull_group2_name = CNT
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = distance ; simple distance increase
pull_coord1_dim = N N Y
pull_coord1_groups = 1 2
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 20 ; kJ mol^-1 nm^-2
进行500ps模拟后使用VMD观看轨迹，发现钠原子并不往碳纳米管方向移动，而是沿着反方向移动。
使用 pull_coord1_type = constant-force 后，钠原子只会被拉动至碳纳米管的质心处，而不会穿过整个碳纳米管。
在lammps中，使用fix smd cation smd cvel 5 0.001 tether NULL NULL -30 0.0 就可以让钠离子穿过碳纳米管，我想请教一下：
1、在GMX中如何实现拉动（最好是umbrella）钠离子穿过碳纳米管？
2、GMX中的pull指令总是会因为拉动距离超过盒子对应方向距离的0.49倍而报错，这一点除使用gmx editconf -f CNT10x10_3.gro -o CNT_box.gro扩大盒子尺寸外有解决方法吗？
另外，在使用pull_coord1_type = constant-force后，钠离子被拉动至碳纳米管质心附近，使用gmx trjconv -s pull.tpr -f pull.xtc -o conf.gro -sep从轨迹提取帧后使用：title = Umbrella pulling simulation
define = -DPOSRES_B
; Run parameters
integrator = md
dt = 0.002
tinit = 0
nsteps = 50000 ; 100 ps
nstcomm = 10
; Output parameters
nstvout = 5000 ; every 10 ps
nstfout = 5000
nstxout-compressed = 5000
nstenergy = 5000
; Bond parameters
constraint_algorithm = lincs
constraints = all-bonds
continuation = no
; Single-range cutoff scheme
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
rlist = 1.4
rcoulomb = 1.4
rvdw = 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = Berendsen
tc_grps = Protein Non-Protein
tau_t = 0.5 0.5
ref_t = 310 310
; Pressure coupling is on
;Pcoupl = Berendsen
;pcoupltype = isotropic
;tau_p = 1.0
;compressibility = 4.5e-5
;ref_p = 1.0
;refcoord_scaling = com
freezegrps = CNT
freezedim = N N Y
; Generate velocities is on
gen_vel = yes
gen_temp = 310
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr = EnerPres
; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = NA
pull_group2_name = CNT
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = distance ; simple distance increase
pull_coord1_dim = N N Y
pull_coord1_groups = 1 2
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = 0.0 ; restrain in place
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
进行NPT，然后使用：
title = Umbrella pulling simulation
; Run parameters
integrator = md
dt = 0.002
tinit = 0
nsteps = 5000000 ; 10 ns
nstcomm = 10
; Output parameters
nstxout-compressed = 5000 ; every 10 ps
nstenergy = 5000
; Bond parameters
constraint_algorithm = lincs
constraints = all-bonds
continuation = yes
; Single-range cutoff scheme
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
rlist = 1.4
rcoulomb = 1.4
rvdw = 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = Nose-Hoover
tc_grps = Protein
tau_t = 1.0
ref_t = 310
; Pressure coupling is on
;Pcoupl = Parrinello-Rahman
;pcoupltype = isotropic
;tau_p = 1.0
;compressibility = 4.5e-5
;ref_p = 1.0
;refcoord_scaling = com
freezegrps = CNT
freezedim = N N Y
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr = EnerPres
; Pull code
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = NA
pull_group2_name = CNT
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = distance ; simple distance increase
pull_coord1_dim = N N Y
pull_coord1_groups = 1 2
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = 0.0 ; restrain in place
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
使用gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal进行伞式采样，发现PMF曲线与预期不符
查看histo.xvg曲线发现并没有交联。
请问该如何解决？
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发表于 Post on 2024-6-13 19:21:39
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