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amber 参数

已有 2316 次阅读 2018-6-20 09:32 |系统分类:科研笔记

scee静电比例常数,默认值1.2;scnb范德华比例常数,默认值2.0。一般不需要更改,注意!Amber11之后这两个参数只在拓扑文件中产生,而不在Sander中运行了。

scee

Usage: scee <value>

Allows the user to set/change the value of the electrostatic scaling constant that will be used to scale 1-4 electrostatic interactions. This needs to be set in the prmtop since it was removed from the sander/pmemd input file in Amber11. This will apply <value> to all dihedral terms.

scnb

Usage: scnb <value>

Allows the user to set/change the value of the VDW scaling constant that will be used to scale 1-4 VDW interactions. This needs to be set in the prmtop since it was removed from the sander/pmemd input file in Amber11. This will apply <value> to all dihedral terms.


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ntwx代表每隔多少步向轨迹文件中记录一次坐标,ntwx = 0表示不产生轨迹文件。

ntwx Every ntwx steps, the coordinates will be written to the mdcrd file. If ntwx = 0, no coordinate trajectory file will be written. Default = 0.


ntwe 代表每隔多少步向mden文件中记录一次能量,ntwe = 0表示不产生mden文件。

ntwe Every ntwe steps, the energies and temperatures will be written to file "mden" in a compact form


ntwr 代表每隔多少步记录一次rst文件,这可以减小MD中途中断导致的损失。

ntwr Every ntwr steps during dynamics, the “restrt” file will be written, ensuring that recovery from a crash will not be so painful.


ntpr 代表每隔多少步向mdout和mdinfo文件中记录一次能量信息,ntwe = 0表示不产生mden文件。

ntpr Every ntpr steps, energy information will be printed in human-readable form to files "mdout" and"mdinfo".


ntwv 代表每隔多少步向mdvel文件中记录一次速度,ntwv = 0表示不产生该文件,ntwv=-1表示将速度记录到mdcrd文件中,这时轨迹文件同时包含速度和坐标。注意,该数据只产生在NetCDF文件中,大多数读者不需要此功能。频繁的读取速度会使得MD运行变慢,影响并行拓展。

ntwv Every ntwv steps, the velocities will be written to the mdvel file. If ntwv = 0, no velocity trajectoryfile will be written. If ntwv = -1, velocities will be written to mdcrd, which then becomes a combined coordinate/velocity trajectory file, at the interval defined by ntwx. This option is available only for binary NetCDF output (ioutfm = 1). Most users will have no need for a velocity trajectory file and so can safely leave ntwv at the default. Default = 0. Note that dumping velocities frequently, like forces or coordinates, will introduce potentially significant I/O and communication overhead, hurting both performance and parallel scaling.


ntwprt代表记录前多少个原子的坐标到轨迹文件中,这个功能可以只保留关注部分的轨迹变化,可以有效减小轨迹文件的大小。比如只保留蛋白的轨迹,而不考虑水分子的轨迹。 

ntwprt The number of atoms to include in trajectory files (mdcrd and mdvel).


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