-dt <每隔多长时间提取一次信息，单位ps>。例如gmx trjconv -f XX.xtc -s XX.gro -dt 100 -o ...
2.1.使用GMX直接导出某一帧坐标我使用命令gmx trjconv -s heat.tpr -f heat.xtc -o QM.pdb -sep...
gmx trjconv [-f[<.xtc/.trr/...>]] [-s[<.tpr/.gro/...>]] [-n[<.ndx>]] [-fr[<.ndx>]] [-sub[<.ndx>]] [-drop[<.xvg>]] [-o[<.xtc/.trr/...>]] [-b<time>] [-e<time>] [-tu<enum>] [-[no]w] [-xvg<enum>] [-skip<int>] [-dt<time>] [-[no]round]...
现在我们可以对我们新生成的轨迹进行截断, 使用trjconv去除前10 ns. -b选项设定要创建的新xtc文件的开始时间, 单位为ps, 这意味着我们需要新文件从10 ps开始. -dt选项指定我们要保留的时间精度. 当提示选择时, 选择Protein来生成xtc文件. gmxtrjconv-ftraj_helix.xtc-otraj_helix_10-50ns.xtc-nXXXX_peptide_...
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当提示选择trjconv的输出组时, 选择蛋白Protein(组1)从而忽略溶剂与离子.(提示: 如前面所述, 可以使用echo来传递选项: echo 1 | trjconv ...) gmxtrjconv-stopol.tpr-ftraj.xtc-oprotein.pdb-pbcnojump-dt50 在PyMOL中载入轨迹 pymolprotein.pdb ...
第一步处理轨迹:gmx_mpi trjconv -f md.xtc -s md.tpr -o md_pbcwhole.xtc -pbc whole ,输出选0 System,得到的轨迹是whole的,二聚体在溶液中自由游走 第二步:选择一个二聚体中心的原子 gmx_mpi trjconv -f md_pbcwhole.xtc -s md.tpr -o md_pbcwhole_atom.xtc -pbc atom -center -n index....
-clndx writes the frame numbers corresponding to the clusters to the specified index file to be read into trjconv. -cl writes average (with option -av) or central structure of each cluster or writes numbered files with cluster members for a selected set of clusters (with option -wcl, dep...
cagen calc dssp2gp fitmol gmx_hbdat gmx_ir gmx_mmpbsa 1ebz.zip _.bsh gmx_mmpbsa.bsh gmx_puckering jscss matchmol model pipistack remd_tgenerator trr2all wvmd xff xpm2all README.md _config.yml index.html markdeep.js Latest commit ...
2.1.使用GMX直接导出某一帧坐标我使用命令gmx trjconv -s heat.tpr -f heat.xtc -o QM.pdb -sep...