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将em.gro（己烷包裹水滴）与金板组合起来进行平衡，模拟崩溃显示如下（没有显示Fatal error）： WARNING: Listednonbonded interaction between particles 723371 and 723379 at distance 8.663which is larger than the table limit 2.048 nm. This is likelyeither a 1,4 interaction, or a listed interaction inside a smaller moleculeyou are decoupling during a free energy calculation. Since interactionsat distances beyond the table cannot be computed, they are skippeduntil they are inside the table limit again. You will only see thismessage once, even if it occurs for several interactions. IMPORTANT: Thisshould not happen in a stable simulation, so there is probably somethingwrong with your system. Only change the table-extension distance in the mdpfile if you are really sure that is the reason. Step 0 Warning: pressure scaling more than 1%, mu:36506.7 36506.7 36506.7 step 0
初始结构（红色为金板（AU），蓝色为己烷，结构中间有两个水滴）和能量最小化后势能曲线如图所示。
除本例失败外，尝试过用共轭梯度法跑能量最小化、减少己烷分子数、调整己烷与金板距离、去掉冻结或控压，均报错。去掉金板，只留己烷和水，能正常平衡和md。请问本例模拟崩溃表明什么，大概率是什么原因，怎么解决，mdp和top文件有错误吗
能量最小化文件em.mdp： define = -DFLEXIBLE integrator = steep nsteps = 1000000 emtol = 100.0 emstep = 0.01 ; nstxout = 100 nstlog = 50 nstenergy = 50 ; pbc = xyz cutoff-scheme = Verlet coulombtype = PME rcoulomb = 1.0 vdwtype = Cut-off rvdw = 1.0 DispCorr = EnerPres ; constraints = none 平衡文件eq.mdp: define = integrator = md dt = 0.001 nsteps = 300000 comm-mode = comm-grps = energygrps = ; nstxout = 1000 nstvout = 1000 nstfout = 1000 nstlog = 1000 nstenergy = 1000 nstxout-compressed =1000 compressed-x-grps = system ; tc_graps = water _ICZ AU annealing = singlesingle single annealing_npoints =2 2 2 annealing_time = 0100 0 100 0 100 annealing_temp = 0298.15 0 298.15 0 298.15 ; pbc = xyz cutoff-scheme =Verlet coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.0 DispCorr = EnerPres ; Tcoupl = V-rescale tau_t = 0.2 0.2 0.2 tc_grps = water _ICZAU ref_t = 298.15 298.15 298.15 ; Pcoupl = Berendsen pcoupltype =isotropic tau_p = 2.0 ref_p = 1.0 compressibility =4.5e-5 ; gen_vel = no gen_temp = 298.15 gen_seed = -1 ; freezegrps = top bottom freezedim = N Y N N Y N constraints = none 拓扑文件如下： #include"gromos54a7_atb.ff/forcefield.itp" #include"gromos54a7_atb.ff/spce.itp" #include"C6H14.itp" [ system ] AUW [ moleculetype ] ; molname nrexcl AU 1 [ atoms ] ; id at type res nr residu name at name cg nr charge mass 1 AU 1 AU AU 1 0.0 196.9665 [ molecules ] SOL 7500 _ICZ 60000
AU 115248
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发表于 Post on 2023-1-30 21:51:17
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发表于 Post on 2023-1-30 23:40:10
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