energygrps = Protein Ligands cutoff-scheme = Verlet coulombtype = cut-off vdwtype = cut-off rcoulomb = 4.0 rvdw = 4.0 GMX不同版本在非键相互作用的设定上有一些差别,上述的设置方式对于我的体系work well。 Method 1中范德华力和库仑力都被分成了短程和长程两项。在截断的方法里,超过截断值的能量...
在mdp中设置energygrps = 聚合物 小分子A/B/C/D/E ，后进行rerun，然后用gmx energy 进行提取...
当前问题和tc_grp毫无关系，要设的显然是energygrps 老师，我按照这个方法计算的组内的非键相互作用项，...
冻结组通过以下两个选项来设置: freezegrps: freezedim:
energygrps = Protein UNK continuation = no constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ns_type = grid nstlist = 5 rlist = 0.9 rcoulomb = 0.9 rvdw = 1.4 coulombtype = PME pme_order = 4 ...
I`m using single precision windows compiled gromacs. I know, I have to change whatever parameter, but so far I didn`t succeed. This is the mdp file: integrator = steepemtol = 1000emstep = 0.01nsteps = 200nstenergy = 10nstxtcout = 10xtc_grps = Proteinenergygrps = Proteinnstlist = ...
\nnstcalcenergy = 10 ;\n\nenergygrps = ;\ncompressed-x-precision = 1000 ;\n;}===\n\n;{ Neighbor searching\n;===\ncutoff-scheme = Verlet ; Verlet Group\nns-type = Grid ; Grid Simple\nnstlist = 1 ;\nrlist = 1.0 ;\
intgmx_anadock(intargc,char*argv[]){constchar*desc[] = {"[THISMODULE] analyses the results of an Autodock run and clusters the","structures together, based on distance or RMSD. The docked energy","and free energy estimates are analysed, and for each cluster the","energy statistics are...
energygrps = A B C D ; 定义四个需要计算能量的组，该组中任意两个组间（除energygrp-table...
energygrps = ;nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 500 nstenergy = 500 nstxout...