1.1. 创建拓扑与坐标文件 gmxeditconf- 编辑模拟盒子以及写入子组(subgroups) gmxprotonate- 结构质子化 gmxx2top- 根据坐标生成原始拓扑文件 gmxsolvate - 体系溶剂化 gmxinsert-molecules- 将分子插入已有空位 gmxgenconf- 增加”随机”取向的构象 gmxgenion - 在能量有利位置加入单原子离子 gmxgenrestr- 生成索引...
dump 1 all xtc 100 dump.xtc 复制代码 这里我设置每隔100步就保存一次轨迹文件。1. 相关软件版本...
$gmx dump" # gmx dump trjconv="$gmx trjconv -dt 1000" # gmx trjconv, use -b -...
Marcello-Sega/gitimPublic Notifications Fork3 Star4 Issues Files ITIM examples maintainer media .travis.yml CMakeLists.txt COPYING DISCLAIMER HOWTO IntrinsicProfilesNutshell.md README.md TUTORIAL.md gmx_dump_vir.cpp gmx_itim.cpp Latest commit ...
$ gmxdump -s yescoupleintramol.tpr >yes.dump $ diff no.dump yes.dump 1c1 < nocoupleintramol.tpr: —- yescoupleintramol.tpr: ### And then also note that this segment of the gmxdump output appears to confirm to me that there is indeed a difference between the A and B state charge...
gmxtrjconv-ftraj_concat_10-50ns-highresolution.xtc-sXXXX_peptide.gro-dump45000-orepresentative_45000ps.pdb 在PyMOL中打开代表性结构以及结合结构, 并比较二者. 其他分析 盐桥 除了氢键之外, 蛋白质不同的带电残基之间也常形成盐桥. 它对蛋白质的结构起着重要的稳定作用, 尤其是当它们处于憎水环境中时, 例...
[DEBUG ] Running command: echo -e "13"| /usr/local/gromacs/bin/gmx trjconv -f md_fit.xtc -s MD.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2024 (-: [DEBUG ] ...
[-abin<real>] [-rbin<real>] [-[no]nitacc] [-[no]contact] [-shell<real>] [-fitstart<real>] [-fitend<real>] [-temp<real>] [-dump<int>] [-max_hb<real>] [-[no]merge] [-acflen<int>] [-[no]normalize] [-P<enum>] [-fitfn<enum>] [-beginfit<real>] [-endfit<real...
(xmgrace)xvg plot formatting: xmgrace, xmgr, none-skip<int>(1)Only write every nr-th frame-dt(0)Only write frame when t MOD dt = first time (ps)-[no]round(no)Round measurements to nearest picosecond-dump(-1)Dump frame nearest specified time (ps)-t0(0)Starting time (ps) (default:...