number of steps for center of mass motion removal nstcomm = 10 ; 对质心进行操作的频率,默认为10 ,单位为[steps] 。 group(s) for center of mass motion removal comm_grps = 对质心进行操作的组,可以是索引文件中的一个,或者多个组。默认为整个系统。
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 ...
(ps), EM不用nsteps = 1000 ; 最大积分步数, 默认0表示无限制comm-mode = Linear ; 移除质心运动的方式, None: 无; Linear: 平动; Angular: 平动转动nstcomm = 10 ; 移除质心运行的频率(步)comm-grps = system ; 移除质心运动的组, 可多个, 默认整个体系tinit = 0 ; 起始时间(ps), EM不用init...
nsteps = 5000000 ; 10ns comm-grps = system energygrps = ; nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 5000 nstenergy = 1000 nstxout-compressed = 1000 compressed-x-grps = system ; pbc = xyz cutoff-scheme = Verlet coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = ...
define=integrator= mddt=0.002; psnsteps=5000000;10nscomm-grps= systemenergygrps= ;nstxout=0nstvout=0nstfout=0nstlog=5000nstenergy=1000nstxout-compressed=1000compressed-x-grps= system;pbc= xyzcutoff-scheme= Verletcoulombtype= PMErcoulomb=1.0vdwtype= cut-offrvdw=1.0DispCorr= EnerPres;Tcoupl= ...
nstcomm = 1 comm_grps = system emtol = 100.0 emstep = 0.01 nstxout = 1 nstvout = 1 nstfout = 1 nstlog = 1 nstenergy = 1 nstxout-compressed= 1 compressed-x-precision= 1000 compressed-x-grps= system energygrps= nstlist = 10 ...
短程neighbor-list截断半径rcoulomb = 1.0 ; 库伦截断半径rvdw = 1.0 ; 范德华力截断半径tc-grps = CNT SOL ;分别进行热浴的类tau_t= 0.1 0.1 ;热浴时间常数( ps )gen_ vel= no ; no :初始速度为零 yes :按照麦克斯韦分布设定初始速度gen_ temp = 300.0 ;麦...
nstcomm = 10 comm-grps = system nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 500 nstenergy = 500 nstxtcout = 1000 xtc_grps = system freezegrps = left right freezedim = Y Y Y Y Y Y ; nstlist = 10 ns_type = grid ...
comm-grps = System ;; Output control ;nstfout = 100000 nstxout = 100000 nstvout =...
dt = 0.001 ; 2 fs comm-grps = Protein comm-mode = angular ; Output control ...