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使用讲义中的水和尿素两相体系进行md过程，是没有报错的，证明我的操作基本是行得通的。
自己使用表面活性剂，如CTAB以insert-molecules的方式向盒子中加入分子，再进行MD，整个过程是行得通的，结果中也观察得到了球形胶束。。
但自己进行表面活性剂，使用packmol建模后进行操作，就出现了错误。具体如下：
① 以MS画出了CTAB的分子式，存为pdb格式， ③ 将MS得到的CTAB.pdb，使用packmol建立一个圆柱状的模型，其中CTAB不是很致密， tolerance 2.0 add_box_sides 1.2 output mix.pdb structure CTAB.pdb number 100 inside cylinder 0. 0. 0. 100. 0. 0. 30. 100. end structure
得到圆柱的pdb文件如图所示，
④ 加入水 gmx solvate -cp mix.pdb -cs tip4p.gro -p CTAB_GMX.top -o CTAB_solv.gro
修改top文件中的CTAB为100 引入力场 #include "oplsaa.ff/forcefield.itp" #include "CTAB_GMX.itp" #include "oplsaa.ff/tip4p.itp"
⑤能量最小 #初步觉得能量最小这一步有问题，但是看起来，自己又看不出问题 define = integrator = steep emtol = 100.0 emstep = 0.01 nsteps = 10000 ; output frequency nstxout = 5000 nstvout = 5000 nstfout = 5000 nstlog = 5000 nstenergy = 5000 nstxtcout =5000 xtc_grps = system nstlist = 10 pbc = xyz rlist = 1.2 cutoff-scheme = Verlet coulombtype = PME rcoulomb = 1.2 vdwtype = cut-off rvdw = 1.2 DispCorr = EnerPres constraints = none constraint_algorithm = LINCS implicit_solvent = no E_x = E_y = E_z =
gmx grompp -f em.mdp -c CTAB_solv.gro -p CTAB_GMX.top -o CTAB.tpr -maxwarn 2 gmx mdrun -deffnm CTAB -v
⑥加入离子，使电荷平衡 gmx genion -s CTAB.tpr -o CTAB-b4em.gro -neutral -p CTAB_GMX.top
再向top里面加入 #include "oplsaa.ff/ions.itp"
再进行能量最小 gmx grompp -f em.mdp -c CTAB-b4em.gro -p CTAB_GMX.top -o em-sol.tpr gmx mdrun -deffnm em-sol –v
得到potential
⑦ 进行nvt预平衡 ;define= cutoff-scheme= Verlet integrator= md dt = 0.001 nsteps = 50000 nstxout= 500 nstvout= 500 nstenergy= 500 nstlog= 500 energygrps =system nstlist= 10 ns_type = grid pbc= xyz rlist= 1.0 coulombtype= PME pme_order= 4 fourierspacing= 0.16 rcoulomb= 1.0 vdw-type= Cut-off rvdw= 1.0 tcoupl = v-rescale tc-grps= system tau_t= 0.1 ref_t= 300 DispCorr= EnerPres pcoupl = no gen_vel = no gen_temp = 300 gen_seed = -1 constraints = hbonds continuation= no constraint_algorithm= lincs lincs_iter = 1 lincs_order= 4
出现错误 Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.080675, max 3.668313 (between atoms 8436 and 8461) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length
Back Off! I just backed up step0b.pdb to ./#step0b.pdb.1#
Back Off! I just backed up step0c.pdb to ./#step0c.pdb.1# Wrote pdb files with previous and current coordinates starting mdrun 'CTABMS in water' 50000 steps, 50.0 ps.
WARNING: Listed nonbonded interaction between particles 8314 and 8317 at distance 2.225 which is larger than the table limit 2.098 nm.
This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions.
IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason.
WARNING: Listed nonbonded interaction between particles 6651 and 6654 at distance 2.126 which is larger than the table limit 2.098 nm.
This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions.
IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason.
WARNING: Listed nonbonded interaction between particles 7999 and 8030 at distance 2.285 which is larger than the table limit 2.098 nm.
This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions.
IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason.
------------------------------------------------------- Program: gmx mdrun, version 2019.6 Source file: src\gromacs\mdlib\sim_util.cpp (line 752)
Fatal error: Step 0: The total potential energy is 3.16378e+17, which is extremely high. The LJ and electrostatic contributions to the energy are 3.1618e+17 and -447610, respectively. A very high potential energy can be caused by overlapping interactions in bonded interactions or very large coordinate values. Usually this is caused by a badly- or non-equilibrated initial configuration, incorrect interactions or parameters in the topology. #我知道是结构不合理导致的能量太大，但自己又不会手动去排除不合理的地方。
For more information and tips for troubleshooting, please check the GROMACS -------------------------------------------------------
初步觉得是建立的模型有错，或者加水的时候，溶剂和溶质分子靠的太近，但是看起来没有什么明显错误，请教如何去排除不合理的地方
解决办法：在win下建立的模型，比centos下建立的模型更容易出错。相同的参数设置，在win下由于能量太大无法进行，但在centos下进行建模，就可能顺利进行。
另外，如果建立模型中分子数太多，双精度gromacs可以解决，在使用双精度能量最小化以后，再改用单精度版本进行mdrun是可行的。
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发表于 Post on 2021-1-24 17:06:14
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发表于 Post on 2021-1-24 18:11:33
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