tcoupl = V-rescale tc_grps = Protein non-Protein tau_t = 1.0 1.0 ref_t = 310.0 310.0 pcoupl = Berendsen pcoupltype = isotropic tau_p = 0.5 ; time constant (ps) ref_p = 1.0 ; reference pressure (bar) compressibility = 4.5e-05 ; isothermal compressibility of water (bar^-1) refc...
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 ...
没有看到C-rescale压浴推荐的常用的时间常数，tau_p ，老师推荐多少呢，以及C-rescale压浴有什么注意...
gmx grompp -f md.mdp -c em.gro -p gc5ay_GMX.top -o md.tprgmx mdrun -v -deffnm md 供参考的脚本文件md.mdp define=integrator= mddt=0.002; psnsteps=5000000;10nscomm-grps= systemenergygrps= ;nstxout=0nstvout=0nstfout=0nstlog=5000nstenergy=1000nstxout-compressed=1000compressed-x-grps=...
tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 ref_p = 1.0 compressibility = 4.5e-5 pbc = xyz DispCorr = EnerPres gen_vel = no The modules grompp and mdrun will be applied just...
cmake-DCMAKE_C_COMPILER=mpicc-DCMAKE_CXX_COMPILER=mpicxx-DGMX_MPI=on. Typical installation As above, and with further details below, but you should consider using the followingCMake optionswith the appropriate value instead ofxxx: -DCMAKE_C_COMPILER=xxxequal to the name of the C99Compiler...
使用gro文件的值; yes: 随机产生gen-temp = 298.15 ; 随机速度对应的温度gen-seed = -1 ; 随机数种子; -1: 自动确定tcoupl = v-rescale ; 耦合方法, no:无; v-rescale: 快速; nose-hoover: 精确tc-grps = system ; 温度耦合组, 可多个tau-t = 2 ; 时间常数(ps)ref-t = 298.15 ; 参考温度(...
tcoupl = v-rescale nsttcouple = 10 tc-grps = System tau-t = 0.1 ref-t = 300 qmmm-cp2k-active = true qmmm-cp2k-qmgroup = QMatoms qmmm-cp2k-qmmethod = INPUT ;PBE ;qmmm-cp2k-qmcharge = -3 ;qmmm-cp2k-qmmultiplicity = 1 ...
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 ...
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 ...