Intro gmx energy能够计算的分子间相互作用主要分为两块:范德华相互作用和库伦相互作用。其中范德华相互作用随距离的增加而衰减很快,因而可以认为是一种短程的相互作用;而库伦相互作用随距离的增加而衰减较慢,…
gmx energy [-f [<.edr>]] [-f2 [<.edr>]] [-s [<.tpr>]] [-o [<.xvg>]] [-viol [<.xvg>]] [-pairs [<.xvg>]] [-corr [<.xvg>]] [-vis [<.xvg>]] [-evisco [<.xvg>]] [-eviscoi [<.xvg>]] [-ravg [<.xvg>]] [-odh [<.xvg>]] [-b ] [-e ] [-[no...
gmx enemat extracts an energy matrix from the energy file (-f). With -groups a file must be supplied with on each line a group of atoms to be used.
I could set up the energy_grp and calculate energy between the ligand group and the lipid layer group. But I need the intramolecular energy in the groups. How should I deal with these problems? Best, Chia-yun Chang -- gmx-users mailing list gmx-users@gromacs.orghttp://lists.gromacs.org...
> But I need the intramolecular energy in the groups. > How should I deal with these problems? > An inter-group energy doesn't mean anything much, so don't bother. Please read the whole of this threadhttp://lists.gromacs.org/pipermail/gmx-users/2010-November/055687.htmlMark ...
如题，contact map的绘制的话，gmx有自带的程序可以完成绘制吗。另外关于FES图，主要是自由能如何计算呢...
Bug summary Running the following command for using "Prot-Lig-CHARMM" system mmpbsa.in file gmx_MMPBSA -O -i mmpbsa.in -cs MD.tpr -ci index.ndx -cg 1 13 -ct md_fit.xtc -cp topol.top but didn't successfully run. ###...
登录 gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS 作者:Valdes-Tresanco, Mario S.; Valdes-Tresanco, Mario E.; Valiente, Pedro A.; Moreno, Ernesto* 来源:Journal of Chemical Theory and Computation, 2021, 17(10): 6281-6291. ...
1-c:最后使用培训书上写的gmx energy的方法计算60个F3分子的相互作用能，具体操作为将60个F3分子分为...
图1所示；也用刚装上的gmx_MMPBSA计算了两者的结合能（binding energy），为图2所示。想问一下大家...