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 water (bar^-1) ;--- ; VELOCITY GENERATION ;--- gen_vel = no ; Veloc...
tau_p–压力耦合的时间常数(单位ps)。 compressibility–溶剂在每bar的可压缩性(上面的设置是水在300K和1大气压下的可压缩性)。 ref_p–压力耦合的参照压力(单位bar,1大气压~ 0.983 bar)。 grompp –f pr.mdp –c fws_b4pr.pdb –p fws.top –o pr.tpr –maxwarn 3 nohup mdrun –s pr.tpr –o ...
tau_p = 2.0 ref_p = 1.0 compressibility = 4.5e-5 refcoord_scaling = com pbc = xyz DispCorr = EnerPres gen_vel = no The modules grompp and mdrun will be called just as we did for NVT equilibration. gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr gmx...
pcoupl = Parrinello-Rahman ; pressure coupling is onforNPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p =2.0; time constant, in ps ref_p =1.0; reference pressure, in bar compressibility =4.5e-5; isothermal compressibility of water, bar^-1refcoord_scaling = com ; Periodi...
tau_t = 0.1 0.1 ; #热偶合时间常数 ref_t = 300 300 ; #参考温度--恒温值,个数对应组 ; Pressure coupling pcoupl = Parrinello-Rahman ; #指定压力耦合方式 ;Parrinello-Rahman: pcoupltype = isotropic ; #isotropic:盒子各向同性 tau_p = 2.0 ; #压力耦合时间常数 ...
tau_p = 1.0 (耦合时间常数 1ps) compressibility = 4.5e-5 (可压缩性,水在一个大气压时为此值) ref_p = 1.0 (耦合参考气压,1个大气压) gen_vel = yes ; gen_temp = 300.0 ; gen_seed = 9999 ; constraints = all-bonds Production MD ...
p=1.0改为tau_p=3.0，可以模拟一段时间，但是稍后又出现这个问题，所以我想问一下tau_p应该在...
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。首先删除旧的 fws_em.tpr 文件,然后运行下面的 grompp命令: grompp –f em.mdp –c fws_ion.pdb –p fws.top –o fws_em.tpr 9 nohup mdrun –v –s fws_em.tpr –o fws...
Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 --- 命令格式 grompp -f pr -c MOL_b4pr -r MOL_b4pr -p MOL -o MOL_pr >& ! output.grompp_pr ### ### MDRUN PR ##...
;Pcoupl = berendsen ;NO:无压力耦合,盒子尺寸大小固定,berendsen:每个时间步长都会重新度量盒子大小,Parrinello-Rahman ;Pcoupltype =semiisotropic ;tau_p = 1.0 1.0 ;耦合时间常数 ;compressibility = 0 4.5e-5 ;压缩系数 ;ref_p =1.0 1.0 ;参考压强 ; Generate velocites is off at 300 K. gen_vel =...