运行完：gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt....
首先是在执行gmx grompp -f ×××.mdp -c R245famix_GMX.gro -p R245famix_GMX.top -o em....
grompp-fnvt.mdp-ptopol_spce.top-cnpt.gro-onvt.tpr mdrun-v -deffnmnvt 第九步:分析数据。我们需要计算CO2的扩散系数。首先,我们需要将周期性边界条件进行unfolding,因为粒子很有可能会跑到盒子外面去,所以运行路程需要累加。 指令为:trjconv-snvt.tpr-fnvt.xtc-onvt_noPBC.xtc-pbcmol-ur compact 其次,做...
minim.mdp ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) ;emtol = 1000.0 ; Stop minimization when the maximum force <1000.0 kJ/mol/nm em...
>> ; minim.mdp - used as input into grompp to generate em.tpr >> ; Parameters describing what to do, when to stop and what to save >> integrator = steep ; Algorithm (steep = steepest descent >> minimization) >> ;emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 ...
(using vi or other file editors): integrator = steep nsteps = 2000 emtol = 1000.0 grompp -f em1.mdp -po -c fbp_sol.gro -p fbp.top -o em1.tpr -v -nice 0 mdrun -s em1.tpr -o em1.trr -c fbp_em1.gro -e em1.edr -g em1.log -v -nice 0 What is the initial and ...
; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) ;emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 ...