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标题: 伞形采样模拟grompp报错求助 [打印本页]

作者
Author: gxs 时间: 2023-5-20 16:32
标题: 伞形采样模拟grompp报错求助
gmx grompp -f npt_umbrella.mdp -c conf6.gro -p topol.top -r conf6.gro -n index.ndx -o npt0.tpr，输入该命令，mdp文件如下所示，出现图一的报错，然后在mdp末尾加入末尾pull_group1_pbcatom = 1，出现如图2的报错
title = Umbrella pulling simulation define = -DPOSRES_B; Run parametersintegrator = mddt = 0.002tinit = 0nsteps = 50000 ; 100 ps nstcomm = 10; Output parametersnstvout = 5000 ; every 10 ps nstfout = 5000nstxout-compressed = 5000nstenergy = 5000; Bond parametersconstraint_algorithm = lincsconstraints = all-bondscontinuation = no ; Single-range cutoff schemecutoff-scheme = Verletnstlist = 20ns_type = grid rlist = 1.4rcoulomb = 1.4rvdw = 1.4; PME electrostatics parameterscoulombtype = PMEfourierspacing = 0.12fourier_nx = 0fourier_ny = 0fourier_nz = 0pme_order = 4ewald_rtol = 1e-5optimize_fft = yes; Berendsen temperature coupling is on in two groupsTcoupl = Berendsen tc_grps = Protein Non-Protein tau_t = 0.5 0.5ref_t = 310 310; Pressure coupling is onPcoupl = Berendsen pcoupltype = isotropictau_p = 1.0 compressibility = 4.5e-5ref_p = 1.0refcoord_scaling = com; Generate velocities is on gen_vel = yes gen_temp = 310; Periodic boundary conditions are on in all directionspbc = xyz; Long-range dispersion correctionDispCorr = EnerPres; Pull codepull = yespull_ncoords = 1 ; only one reaction coordinatepull_ngroups = 2 ; two groups defining one reaction coordinatepull_group1_name = Chain_Apull_group2_name = Chain_Bpull_coord1_type = umbrella ; harmonic potentialpull_coord1_geometry = distance ; simple distance increasepull_coord1_dim = N N Ypull_coord1_groups = 1 2pull_coord1_start = yes ; define initial COM distance > 0pull_coord1_rate = 0.0 ; restrain in place pull_coord1_k = 1000 ; kJ mol^-1 nm^-2pull_group1_pbcatom = 1

作者
Author: Frozen-Penguin 时间: 2023-5-21 13:48
这是周期性边界条件下计算质心的要求，计算质心的组尺寸如果太大，就无法正确计算质心，解决方法是加大盒子的尺寸。

作者
Author: gxs 时间: 2023-5-23 17:10

Frozen-Penguin 发表于 2023-5-21 13:48
这是周期性边界条件下计算质心的要求，计算质心的组尺寸如果太大，就无法正确计算质心，解决方法是加大盒子 ...

好的，谢谢。那请问该怎么判断加多少大小的盒子呢

作者
Author: Frozen-Penguin 时间: 2023-5-24 22:49
如报错信息所说，需要group中所有原子的距离到PBC atom（默认是组内的第一个原子）的距离小于盒子尺寸的一半。

作者
Author: gxs 时间: 2023-6-6 17:30
盒子有三个方向x,y,z 请问需要每个方向都满足吗

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