分析梳理--分子动力学模拟的常规步骤四（Gromacs）

;em_real.mdp-grompp的参数输入文件
integrator = steep;指定使用最陡下降法进行能量最小化.若设为cg则使用共轭梯度法;
emtol = 1000.0 ;若力的最大值小于此值则认为能量最小化收敛k/mol/nm.
emstep=0.01;初始步长
nsteps= 50000;在能量最小化中，指定最大迭代次数

; 近邻列表, 相互作用计算参数
nstlist    = 1    ; 更新近邻列表的频率. 1 表示每步都更新
cutoff-scheme = Verlet ; 生成带有缓冲的对列表。 (5.1后) 没有水更快
ns_type    = grid   ; 近邻列表的确定方法，适用于大体系
coulombtype  = PME   ; 计算长程静电的方法.PME为粒子网格 Ewald 方法
rcoulomb   = 1.0    ; 长程库仑力的截断值
rvdw    = 1.0    ; 范德华距离截断值
pbc    = xyz    ; 在所有方向上使用周期性边界条件。

gmx grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o em.tpr

Options to specify input files:

 -s      [<.tpr>]           (topol.tpr)
           Portable xdr run input file
 -cpi    [<.cpt>]           (state.cpt)      (Opt.)
           Checkpoint file
 -table  [<.xvg>]           (table.xvg)      (Opt.)
           xvgr/xmgr file
 -tablep [<.xvg>]           (tablep.xvg)     (Opt.)
           xvgr/xmgr file
 -tableb [<.xvg> [...]]     (table.xvg)      (Opt.)
           xvgr/xmgr file
 -rerun  [<.xtc/.trr/...>]  (rerun.xtc)      (Opt.)
           Trajectory: xtc trr cpt gro g96 pdb tng
 -ei     [<.edi>]           (sam.edi)        (Opt.)
           ED sampling input
 -multidir [<dir> [...]]    (rundir)         (Opt.)
           Run directory
 -awh    [<.xvg>]           (awhinit.xvg)    (Opt.)
           xvgr/xmgr file
 -plumed [<.dat>]           (plumed.dat)     (Opt.)
           Generic data file
 -membed [<.dat>]           (membed.dat)     (Opt.)
           Generic data file
 -mp     [<.top>]           (membed.top)     (Opt.)
           Topology file
 -mn     [<.ndx>]           (membed.ndx)     (Opt.)
           Index file

Options to specify output files:

 -o      [<.trr/.cpt/...>]  (traj.trr)
           Full precision trajectory: trr cpt tng
 -x      [<.xtc/.tng>]      (traj_comp.xtc)  (Opt.)
           Compressed trajectory (tng format or portable xdr format)
 -cpo    [<.cpt>]           (state.cpt)      (Opt.)
           Checkpoint file
 -c      [<.gro/.g96/...>]  (confout.gro)
           Structure file: gro g96 pdb brk ent esp
 -e      [<.edr>]           (ener.edr)
           Energy file
 -g      [<.log>]           (md.log)
           Log file
 -dhdl   [<.xvg>]           (dhdl.xvg)       (Opt.)
           xvgr/xmgr file
 -field  [<.xvg>]           (field.xvg)      (Opt.)
           xvgr/xmgr file
 -tpi    [<.xvg>]           (tpi.xvg)        (Opt.)
           xvgr/xmgr file
 -tpid   [<.xvg>]           (tpidist.xvg)    (Opt.)
           xvgr/xmgr file
 -eo     [<.xvg>]           (edsam.xvg)      (Opt.)
           xvgr/xmgr file
 -px     [<.xvg>]           (pullx.xvg)      (Opt.)
           xvgr/xmgr file
 -pf     [<.xvg>]           (pullf.xvg)      (Opt.)
           xvgr/xmgr file
 -ro     [<.xvg>]           (rotation.xvg)   (Opt.)
           xvgr/xmgr file
 -ra     [<.log>]           (rotangles.log)  (Opt.)
           Log file
 -rs     [<.log>]           (rotslabs.log)   (Opt.)
           Log file
 -rt     [<.log>]           (rottorque.log)  (Opt.)
           Log file
 -mtx    [<.mtx>]           (nm.mtx)         (Opt.)
           Hessian matrix
 -if     [<.xvg>]           (imdforces.xvg)  (Opt.)
           xvgr/xmgr file
 -swap   [<.xvg>]           (swapions.xvg)   (Opt.)
           xvgr/xmgr file

Other options:

 -deffnm <string>
           Set the default filename for all file options
 -xvg    <enum>             (xmgrace)
           xvg plot formatting: xmgrace, xmgr, none
 -dd     <vector>           (0 0 0)
           Domain decomposition grid, 0 is optimize
 -ddorder <enum>            (interleave)
           DD rank order: interleave, pp_pme, cartesian
 -npme   <int>              (-1)
           Number of separate ranks to be used for PME, -1 is guess
 -nt     <int>              (0)
           Total number of threads to start (0 is guess)
 -ntmpi  <int>              (0)
           Number of thread-MPI ranks to start (0 is guess)
 -ntomp  <int>              (0)
           Number of OpenMP threads per MPI rank to start (0 is guess)
 -ntomp_pme <int>           (0)
           Number of OpenMP threads per MPI rank to start (0 is -ntomp)
 -pin    <enum>             (auto)
           Whether mdrun should try to set thread affinities: auto, on, off
 -pinoffset <int>           (0)
           The lowest logical core number to which mdrun should pin the first
           thread
 -pinstride <int>           (0)
           Pinning distance in logical cores for threads, use 0 to minimize
           the number of threads per physical core
 -gpu_id <string>
           List of unique GPU device IDs available to use
 -gputasks <string>
           List of GPU device IDs, mapping each task on a node to a device.
           Tasks include PP and PME (if present).
 -[no]ddcheck               (yes)
           Check for all bonded interactions with DD
 -rdd    <real>             (0)
           The maximum distance for bonded interactions with DD (nm), 0 is
           determine from initial coordinates
 -rcon   <real>             (0)
           Maximum distance for P-LINCS (nm), 0 is estimate
 -dlb    <enum>             (auto)
           Dynamic load balancing (with DD): auto, no, yes
 -dds    <real>             (0.8)
           Fraction in (0,1) by whose reciprocal the initial DD cell size will
           be increased in order to provide a margin in which dynamic load
           balancing can act while preserving the minimum cell size.
 -nb     <enum>             (auto)
           Calculate non-bonded interactions on: auto, cpu, gpu
 -nstlist <int>             (0)
           Set nstlist when using a Verlet buffer tolerance (0 is guess)
 -[no]tunepme               (yes)
           Optimize PME load between PP/PME ranks or GPU/CPU
 -pme    <enum>             (auto)
           Perform PME calculations on: auto, cpu, gpu
 -pmefft <enum>             (auto)
           Perform PME FFT calculations on: auto, cpu, gpu
 -bonded <enum>             (auto)
           Perform bonded calculations on: auto, cpu, gpu
 -update <enum>             (auto)
           Perform update and constraints on: auto, cpu, gpu
 -[no]v                     (no)
           Be loud and noisy
 -pforce <real>             (-1)
           Print all forces larger than this (kJ/mol nm)
 -[no]reprod                (no)
           Avoid optimizations that affect binary reproducibility; this can
           significantly reduce performance
 -cpt    <real>             (15)
           Checkpoint interval (minutes)
 -[no]cpnum                 (no)
           Keep and number checkpoint files
 -[no]append                (yes)
           Append to previous output files when continuing from checkpoint
           instead of adding the simulation part number to all file names
 -nsteps <int>              (-2)
           Run this number of steps (-1 means infinite, -2 means use mdp
           option, smaller is invalid)
 -maxh   <real>             (-1)
           Terminate after 0.99 times this time (hours)
 -replex <int>              (0)
           Attempt replica exchange periodically with this period (steps)
 -nex    <int>              (0)
           Number of random exchanges to carry out each exchange interval (N^3
           is one suggestion).  -nex zero or not specified gives neighbor
           replica exchange.
 -reseed <int>              (-1)
           Seed for replica exchange, -1 is generate a seed

gmx mdrun -ntmpi 4 -ntomp 17 -v -deffnm em

gmx energy -f em.edr -o potential.xvg