喵星大佬 发表于 2022-3-8 16:17 是这一步不应该设置pme gpu……去掉之后后面就正常了 |
喵星大佬 发表于 2022-3-8 16:17 啊是的，极小化那一步就卡住了 （谢谢回复！） |
sobereva 发表于 2022-3-8 22:10 老师好，谢谢回复！！ mdp如下： 1）step6.0_minimization.mdp define = -DPOSRES -DPOSRES_FC_BB=4000.0 -DPOSRES_FC_SC=2000.0 -DPOSRES_FC_LIPID=1000.0 -DDIHRES -DDIHRES_FC=1000.0 integrator = steep emtol = 1000.0 nsteps = 5000 nstlist = 10 cutoff-scheme = Verlet rlist = 1.2 vdwtype = Cut-off vdw-modifier = Force-switch rvdw_switch = 1.0 rvdw = 1.2 coulombtype = PME rcoulomb = 1.2 ; constraints = h-bonds constraint_algorithm = LINCS 2）step6.6_equilibration.mdp define = -DPOSRES -DPOSRES_FC_BB=50.0 -DPOSRES_FC_SC=0.0 -DPOSRES_FC_LIPID=0.0 -DDIHRES -DDIHRES_FC=0.0 integrator = md dt = 0.002 nsteps = 250000 nstxtcout = 5000 nstvout = 5000 nstfout = 5000 nstcalcenergy = 100 nstenergy = 1000 nstlog = 1000 ; cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 vdwtype = Cut-off vdw-modifier = Force-switch rvdw_switch = 1.0 rvdw = 1.2 coulombtype = PME rcoulomb = 1.2 ; tcoupl = berendsen tc_grps = SOLU MEMB SOLV tau_t = 1.0 1.0 1.0 ref_t = 294.15 294.15 294.15 ; pcoupl = berendsen pcoupltype = semiisotropic tau_p = 5.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 refcoord_scaling = com ; constraints = h-bonds constraint_algorithm = LINCS continuation = yes ; nstcomm = 100 comm_mode = linear comm_grps = SOLU_MEMB SOLV 3）step7_production.mdp integrator = md dt = 0.002 nsteps = 500000 nstxout = 50000 nstvout = 50000 nstfout = 50000 nstcalcenergy = 100 nstenergy = 1000 nstlog = 1000 ; cutoff-scheme = Verlet nstlist = 20 rlist = 1.2 vdwtype = Cut-off vdw-modifier = Force-switch rvdw_switch = 1.0 rvdw = 1.2 coulombtype = PME rcoulomb = 1.2 ; tcoupl = Nose-Hoover tc_grps = SOLU MEMB SOLV tau_t = 1.0 1.0 1.0 ref_t = 294.15 294.15 294.15 ; pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 ; constraints = h-bonds constraint_algorithm = LINCS continuation = yes ; nstcomm = 100 comm_mode = linear comm_grps = SOLU_MEMB SOLV |
| 把mdp贴出来 |
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