求助：关于mdp文件中awh选项的设置问题

wanzongliang

我想用gromacs模拟在xy方向上俩个分子之间的PMF，设置mdp文件后grompp出现如下报错
ERROR 1 [file awh1_1.mdp, line 85]:
  One pull coordinate (1) cannot be mapped to two separate AWH dimensions
  (awh1-dim1 and awh1-dim2). If this is really what you want to do you will
  have to duplicate this pull coordinate.


ERROR 2 [file awh1_1.mdp, line 85]:
  One pull coordinate (1) cannot be mapped to two separate AWH dimensions
  (awh1-dim2 and awh1-dim1). If this is really what you want to do you will
  have to duplicate this pull coordinate.

想请问一下各位这是什么原因（附上我的mdp文件）

wanzongliang

laoman 发表于 2023-10-31 16:35
pull-coord duplicate之后应该只有pull-coord1和pull-coord2，不知道你的pull-coord3是怎么来的。剩下的 ...

好的万分感谢

laoman

wanzongliang 发表于 2023-10-31 08:55
您好，非常感谢您的回复，我根据您给的选项修改了我的mdp文件但出现了新的报错Command line:
  gmx-2023 ...

pull-coord duplicate之后应该只有pull-coord1和pull-coord2，不知道你的pull-coord3是怎么来的。剩下的还是那句话，理解Error说的意思，结合官网的说明来修改mdp。你这只有一个mdp文件，我也爱莫能助。

wanzongliang

laoman 发表于 2023-10-30 23:01
报错信息的指示很明确，就是复制一下pull coordinates：

您好，非常感谢您的回复，我根据您给的选项修改了我的mdp文件但出现了新的报错Command line:
  gmx-2023.1 grompp -f awh1_1.mdp -c equilibrium.gro -p 4NS_Li_water.top -n index.ndx -po awh1_1ine.mdp -o awh1.tpr

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'optimize_fft'
Ignoring obsolete mdp entry 'ns_type'
Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
Setting the AWH bias MC random seed to -17303889

ERROR 1 [file awh1_1.mdp, line 94]:
  The given AWH coordinate index (3) is larger than the number of pull
  coordinates (2)


ERROR 2 [file awh1_1.mdp, line 94]:
  Setting pull-coord3-rate (3.23219e-40) is incompatible with AWH biasing
  this coordinate

Setting the LD random seed to 2080208251

Generated 364231 of the 364231 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5

Generated 364231 of the 364231 1-4 parameter combinations

Excluding 3 bonded neighbours molecule type 'GO1'

turning H bonds into constraints...

Excluding 3 bonded neighbours molecule type 'GO2'

turning H bonds into constraints...

Excluding 1 bonded neighbours molecule type 'NA'

turning H bonds into constraints...

Excluding 1 bonded neighbours molecule type 'LI'

turning H bonds into constraints...

Excluding 1 bonded neighbours molecule type 'CL'

turning H bonds into constraints...

Excluding 2 bonded neighbours molecule type 'SOL'

turning H bonds into constraints...

-------------------------------------------------------
Program:     gmx grompp, version 2023.1
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2198)

Fatal error:
There were 2 errors in input file(s)

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
我不确定是不是因为我的体系中只加入了一个Li离子导致无法向俩个方向拉伸，请问您知道这是怎么回事吗

laoman

报错信息的指示很明确，就是复制一下pull coordinates：

1. pull                     = yes                 ; The reaction coordinate (RC) is defined using pull coordinates.
   
2. pull-ngroups             = 4                   ; The number of atom groups needed to define the pull coordinate.
   
3. pull-ncoords             = 2                   ; Number of pull coordinates.
   
4. pull-nstxout             = 10000               ; Step interval to output the coordinate values to the pullx.xvg.
   
5. pull-nstfout             = 10000               ; Step interval to output the applied force (skip here).
   
6.                                                
   
7. pull-group1-name         = Li                  ; Name of pull group 1 corresponding to an entry in an index file.
   
8. pull-group2-name         = SO3                 ; Same, but for group 2.
   
9. pull-group3-name         = Li                  ; Name of pull group 1 corresponding to an entry in an index file.
   
10. pull-group4-name         = SO3                 ; Same, but for group 2.
    
11.                                                
    
12. pull-coord1-groups       = 1 2                 ; Which groups define coordinate 1? Here, groups 1 and 2.
    
13. pull-coord1-geometry     = distance            ; How is the coordinate defined? Here by the COM distance.
    
14. pull-coord1-dim          = Y N N
    
15. pull-coord1-start        = yes
    
16. pull-coord1-type         = external-potential  ; Apply the bias using an external module.
    
17. pull-coord1-potential-provider = AWH           ; The external module is called AWH!
    
18. 
    
19. pull-coord2-groups       = 3 4                 ; Which groups define coordinate 1? Here, groups 1 and 2.
    
20. pull-coord2-geometry     = distance            ; How is the coordinate defined? Here by the COM distance.
    
21. pull-coord2-dim          = N Y N
    
22. pull-coord2-start        = yes
    
23. pull-coord2-type         = external-potential  ; Apply the bias using an external module.
    
24. pull-coord2-potential-provider = AWH           ; The external module is called AWH!

复制代码

不确定改得对不对，你可以试试看能不能跑起来。