https://ambermd.org/tutorials/advanced/tutorial4/index.php
这部分主要学习如何限制键长键角二面角。
施加限制的prod.in文件如下:
hold-npt
&cntrl
imin=0,irest=1,ntx=5,
nstlim=50000000,
dt=0.002,ntc=2,ntf=2,
cut=10.0,
ntpr=1, ntwx=1,ntwr=50000,
ntt=3, gamma_ln=2.0,
temp0=300.0,
ntp=2, ntb=2,
ioutfm=1,ntxo=1,
iwrap=1,
ig=-1
nmropt=1
/
&wt type='END' /
LISTOUT=POUT # Getting summaries of NMR violations:在prod.out文件的最后输出 the remaining restraint violations,一般好像没啥用。。。
DISANG=fe.RST
fe.RST文件内容如下:
# Harmonic restraints for the restrained nonbonded model of 7DDQ,# 我这里要限制的是25456 和44926两原子的距离
&rst iat=25456,44926, r1=0., r2=3.464, r3=3.464, r4=100., rk2=580.2, rk3=580.2,/
或者,fe.RST文件可以添加多个距离限制(r1和r4是势能函数的边界值,r2和r3定义了势能函数中间的平滑区域,rk2和rk3分别是左边界和右边界的力常数):
# Harmonic restraints for the restrained nonbonded model of FE cluster
&rst iat=36623,28379, r1=0, r2=2.41, r3=2.41, r4=5, rk2=500, rk3=500/
&rst iat=36623,28970, r1=0, r2=2.47, r3=2.47, r4=5, rk2=500, rk3=500/
&rst iat=36623,35393, r1=0, r2=2.56, r3=2.56, r4=5, rk2=500, rk3=500/
&rst iat=36623,34674, r1=0, r2=2.43, r3=2.43, r4=5, rk2=500, rk3=500/
&rst iat=36623,34891, r1=0, r2=2.33, r3=2.33, r4=5, rk2=500, rk3=500/
&rst iat=36623,34890, r1=0, r2=2.62, r3=2.62, r4=5, rk2=500, rk3=500/
&rst iat=84084,82854, r1=0, r2=2.57, r3=2.57, r4=5, rk2=500, rk3=500/
&rst iat=84084,76431, r1=0, r2=2.47, r3=2.47, r4=5, rk2=500, rk3=500/
&rst iat=84084,75839, r1=0, r2=2.41, r3=2.41, r4=5, rk2=500, rk3=500/
&rst iat=84084,82135, r1=0, r2=2.43, r3=2.43, r4=5, rk2=500, rk3=500/
&rst iat=84084,82351, r1=0, r2=2.62, r3=2.62, r4=5, rk2=500, rk3=500/
&rst iat=84084,82352, r1=0, r2=2.33, r3=2.33, r4=5, rk2=500, rk3=500/
本文来自博客园,作者:计算之道,转载请注明原文链接:https://www.cnblogs.com/jszd/p/15739868.html