19 可以重现 请问社长，comm-grps和comm-mode这两项只需要分别设置为Protein、Angular就可以了吗 ...
tc_grps = Protein non-Protein tau_t = 1.0 1.0 ref_t = 310.0 310.0 pcoupl = Parrinello-Rahman pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 1 ; time constant (ps) ref_p = 1.0 ; reference pressure (bar) compressibility = 4.5e-05 ; isothermal compressibility of wate...
修改Protein_A.itp文件,删除其中72位残基的HG1原子,并将整个文件的原子重新编号,修改键,键角,二面角的原子编号。可参考下述脚本 modifyiptfile.py 进行itp文件修改。 import os from collections import defaultdict class Lig_itp: def __init__(self, lig_itp_file): self.moleculetype = list() self.atoms =...
comm-grps = Protein comm-mode = angular ; Output control nstxout = 5000 ; save coo...
tc-grps=Protein Non-Protein tau_t=0.10.1 ref_t=300300 pcoupl=no pbc=xyz DispCorr=EnerPres gen_vel=yes gen_temp=300 gen_seed=−1 Thegromppandmdrunmodules are used just as we did at the EM step: gmx grompp -f nvt.mdp -c em2.gro -p topol.top -o nvt.tpr ...
（2） tc-grps = protein non-protein 表示的具体意思是什么，我看manul没有很懂，另外我模拟...
加氯离子后的pr_md.mdp和md.mdp文件的温度耦合参数 ;Berendsen temperature coupling using vel rescaling is on Tcoupl = v-rescale tau_t = 0.1 0.1 tc_grps = protein non-protein ref_t = 300 300 记住:如果要加入氯离子,需要重新运行第 6步的grompp。首先删除 15、旧的 fws_em.tpr文件,然后运行...
comm-mode = Linear comm-grps = Protein_HEM_MOL_2FE_4FE_3FE_DPPC SOL_CL ; Scale COM ...
Gromacs模拟基本流程
comm-grps = ;for Langevin Dynamics(bd):bd-temp = (300)[K]bd_fric: = (0)[amu/ps]ld_seed = (1993)[integer];for Energy Minimization:emtol = (100.0)[kJ/(mol*nm)]emstep = (0.01)[nm]nstcgsteep = (1000)[steps]nbfgscorr = (10);for Shell Molecular ...