gmx hbond后接-ac得到的氢键寿命，哪个是直接可用的数据

牧生

近日使用了一个含有884个水分子的纯水盒子，使用了spc水模型跑了一段MD，使用gmx hbond计算氢键，结果发现与预期不合。同时也结合了http://bbs.keinsci.com/thread-28948-1-1.html这个里面的讨论，但始终觉得有点不对

具体情况如下：

第一种情况，使用gmx2024.4顺利跑完MD，然后使用命令为

1. gmx hbond -f prod.xtc -s prod.tpr -num  -life -nhbdist -nomerge

复制代码

发现2024.4或者2025.1都不能读取 -life -nhbdist -nomerge命令

λgmx hbond -f prod.xtc -s prod.tpr -num  -life -nhbdist -nomergee
                      :-) GROMACS - gmx hbond, 2024.4 (-:

Executable:   D:\software\GROMACS2024_4_GPU\bin\gmx.exe
Data prefix:  D:\software\GROMACS2024_4_GPU
Working dir:  C:\Users\Administrator\Desktop\waterbox
Command line:
  gmx hbond -f prod.xtc -s prod.tpr -num -life -nhbdist -nomerge


-------------------------------------------------------
Program:     gmx hbond, version 2024.4
Source file: src\gromacs\commandline\cmdlineparser.cpp (line 271)
Function:    void __cdecl gmx::CommandLineParser::parse(int *,char *[])

Error in user input:
Invalid command-line options
    Unknown command-line option -life
    Unknown command-line option -nhbdist
    Unknown command-line option -nomerge

For more information and tips for troubleshooting, please check the GROMACS
website at https://manual.gromacs.org/curre ... un-time-errors.html


但是如果换用仅含有-num的命令，倒是可以正常结束的，但是得到的结果中只有s0列，没有s1列

1. gmx hbond -f prod.xtc -s prod.tpr -num

复制代码

问题一：如何在高版本的gmx中得到 -life -nhbdist 等结果呢   （已经解决）


第二种情况，使用gmx2022.6跑MD，结束后，使用以下命令就没问题。可以得到s0和s1两列数据，也可以计算得到氢键寿命

1. gmx hbond -f prod.xtc -s prod.tpr -num  -life -nhbdist -nomerge

复制代码

Executable:   D:\software\gmx2022.6_GPU\bin\gmx.exe
Data prefix:  D:\software\gmx2022.6_GPU
Working dir:  C:\Users\Administrator\Desktop\waterbox
Command line:
  gmx hbond -f prod.xtc -s prod.tpr -num -life -nhbdist -nomerge


Back Off! I just backed up nhbdist.xvg to ./#nhbdist.xvg.1#
Reading file prod.tpr, VERSION 2022.6 (single precision)
Specify 2 groups to analyze:
Group     0 (         System) has  2652 elements
Group     1 (          Water) has  2652 elements
Group     2 (            SOL) has  2652 elements
Select a group: 0
Selected 0: 'System'
Select a group: 0
Selected 0: 'System'
Calculating hydrogen bonds in System (2652 atoms)
Found 884 donors and 884 acceptors
Making hbmap structure...done.
Reading frame       0 time    0.000
Will do grid-search on 7x7x7 grid, rcut=0.34999999
Frame loop parallelized with OpenMP using 16 threads.
Last frame        500 time 1000.000
Found 362602 different hydrogen bonds in trajectory
Found 435446 different atom-pairs within hydrogen bonding distance

Back Off! I just backed up hbnum.xvg to ./#hbnum.xvg.1#
Average number of hbonds per timeframe 1532.200 out of 390728 possible

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu
Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media
J. Phys. Chem. B 110 (2006) pp. 4393-4398
-------- -------- --- Thank You --- -------- --------


HB lifetime = 2.19 ps
Note that the lifetime obtained in this manner is close to useless
Use the -ac option instead and check the Forward lifetime

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu
Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media
J. Phys. Chem. B 110 (2006) pp. 4393-4398
-------- -------- --- Thank You --- -------- --------


GROMACS reminds you: "I Smell Smoke From a Gun Named Extinction" (Pixies)





问题二：如红色字体中所示，gmx给出的氢键平均数为1532，那么这个平均，是用什么来取的平均呢？是每一帧的氢键数量之和，除以帧数得到的平均值吗？



红色字体中也说明了，以这种方式计算的氢键寿命几乎没用，应该用-ac，然后检查Forward lifetime。

为了节约时间，重新跑了一个spc216的水盒子，使用命令为

1. gmx hbond-legacy  -f prod.xtc -s prod.tpr -num  -life -nhbdist -nomerge -ac
   

复制代码

得到


Doing autocorrelation according to the theory of Luzar and Chandler.
ACF 30018/30018
Normalization for c(t) = 0.00268054 for gh(t) = 2.65351e-05
Hydrogen bond thermodynamics at T = 298.15 K
Fitting parameters chi^2 = 0.000122375
Q =          0
--------------------------------------------------
Type      Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2
Forward         1.559      0.641       3.427  0.000122375
Backward       -0.002   -466.651    -666.000
One-way         3.095      0.323       1.727
Integral        0.185      5.404       8.710
Relaxation      0.153      6.519       9.175


Back Off! I just backed up hblife.xvg to ./#hblife.xvg.1#
HB lifetime = 5.34 ps
Note that the lifetime obtained in this manner is close to useless
Use the -ac option instead and check the Forward lifetime


问题三：此处，哪个才是真实的氢键寿命呢

student0618

gmx 2024 开始改了hbond指令，用hbond-legacy才是以前版本的gmx hbond