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本帖最后由 Nancylee0416 于 2023-1-18 09:51 编辑
各位大佬求助，Gromacs2021.1，模拟包含两条链蛋白-小分子结构，拉伸其中一条短链，整个蛋白轨迹能看到结构的变化过程。我的理解初始拉力特别大，是否是我拉伸速度太快了。但无论怎么调整拉伸速度和弹簧系数，pullf.xvg的图像都是折线，没有拉伸蓄力然后突然降低这种趋势，force的初始数值很大，上万。
# This file was created Wed Jan 18 02:06:55 2023
# Created by:
# :-) GROMACS - gmx mdrun, 2021.1-UNCHECKED (-:
#
# Executable: /data/apps/gromacs/2021.1/bin/gmx
# Data prefix: /data/apps/gromacs/2021.1
# Working dir: /data/run01/scv74/c6
# Command line:
# gmx mdrun -v -deffnm pull -ntmpi 1 -ntomp 64 -pf pullf.xvg -px pullx.xvg
# gmx mdrun is part of G R O M A C S:
#
# GROningen Mixture of Alchemy and Childrens' Stories
#
@ title "Pull force"
@ xaxis label "Time (ps)"
@ yaxis label "Force (kJ/mol/nm)"
@TYPE xy
0.0000 21700.8
0.1000 418.709
0.2000 -218.96
0.3000 -765.794
0.4000 3215.54
0.5000 3162.72
0.6000 -1794.76
0.7000 2130.37
0.8000 -1687.06
0.9000 -1192.78
1.0000 1150.68
1.1000 -1726.93
1.2000 2013.48
1.3000 -369.352
1.4000 -1420.56
1.5000 -1309.59
1.6000 -815.409
1.7000 -1084.83
1.8000 -1008.61
1.9000 409.044
2.0000 1197.65
2.1000 -1846.54
2.2000 231.067
2.3000 52.0729
2.4000 -1232.94
2.5000 744.321
2.6000 183.353
2.7000 -391.624
2.8000 -691.917
2.9000 1367.23
3.0000 1447.83
附上mdp文件
; title = Umbrella pulling simulation
define = -DPOSRES_A
这部分位置限制需要根据限制哪一个链来调整DPOSRES_A? 我想固定的区域是A链和小分子，在index.ndx中把它设定为A组，但itp文件中只在topol_Protein_chain_A.itp末尾添加限制，这样是否有影响呢？
; Run parameters
integrator = md
dt = 0.002
tinit = 0
nsteps = 500000 ; 1000 ps
nstcomm = 10
comm-mode = Linear
comm-grps = System
; Output parameters
nstxout = 5000 ; every 10 ps
nstvout = 5000
nstfout = 5000
nstxout-compressed = 5000 ; every 10 ps
nstenergy = 5000
; Bond parameters
constraint_algorithm = lincs
constraints = h-bonds
continuation = yes ; continuing from NPT
; 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 = system
tau_t = 1.0
ref_t = 310
; Pressure coupling is on
Pcoupl = Parrinello-Rahman
pcoupltype = isotropic
tau_p = 2.5
compressibility = 4.5e-5
ref_p = 1.0
refcoord_scaling = com
; 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-pbc-ref-prev-step-com = yes
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group1_name = Chain_B
pull-group1-pbcatom = 3212
这个参数我选择了要拉动的B链中的一个任意原子
pull_group2_name = Chain_A
pull-group2-pbcatom = 1395
这个参数我选择了要拉动的A链中的一个任意原子，但Chain_A包括A链和小分子。
pull_ncoords = 1 ; only one reaction coordinate
pull_coord1_type = constraint ; harmonic potential
pull_coord1_geometry = distance ; simple distance increase
pull_coord1_dim = N N Y
;pull_coord1-vec = 0 0 1
pull_coord1_groups = 1 2
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = 0.002
；拉伸速度从0.01修改为0.001,0.002,0.005，都进行了尝试。
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
；弹簧系数从1000调整为500,100，都进行了尝试。
pull-nstxout = 50
pull-nstfout = 50
求助大家！
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发表于 Post on 2023-1-18 09:46:09
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