[gmx-users] constraints using all-angles

[Mark Abraham]

----- Original Message -----
From: Sang-Won Park <icocoon1 at gmail.com>
Date: Monday, May 17, 2010 14:07
Subject: [gmx-users] constraints using all-angles
To: gmx-users at gromacs.org

> Hello,
> 
> I'm trying to do set a configuration for BMIM PF6 with rigid 
> body anion.
> So, I tested all-angles constraints for one molecule of PF6-.
> 
> Below is the conf.gro file.
> -----------------------------------------------------
> PF6
>     7
>     1PF6     
> P1    1   0.000   
> 0.000   0.000
>     1PF6     
> F1    2   0.156   
> 0.000   0.000
>     1PF6     
> F2    3   0.000   
> 0.156   0.000
>     1PF6     
> F3    4   0.000   
> 0.000   0.156
>     1PF6     
> F4    5  -0.156   
> 0.000   0.000
>     1PF6     
> F5    6   0.000  -
> 0.156   0.000
>     1PF6     
> F6    7   0.000   0.000  
> -0.156
>    2.50000   2.50000   2.50000
> 
> -----------------------------------------------------
> 
> And below is a part of .top file. I fix all bonds and the distances
> between fluorine atoms.
> -----------------------------------------------------
> [ moleculetype ]
> ; 
> Name            nrexcl
> PF6                 3
> 
> [ atoms ]
> ;   nr       type  
> resnr residue  atom   
> cgnr     charge       mass
> typeB    chargeB      massB
>      
> 1         P1      1    PF6     P1      1       1.34    30.9738
>      
> 2         F1      1    PF6     F1      1      -0.39   

Why do you have an explicit mass for P and not F? Perhaps grompp is allocating zero mass and this is breaking the constraint algorithm somehow. check the density (or whatever) reported by grompp on its stdout

Mark

> 3         F2      1    PF6     F2      1      -0.39   
>      
> 4         F3      1    PF6     F3      1      -0.39   
>      
> 5         F4      1    PF6     F4      1      -0.39   
>      
> 6         F5      1    PF6     F5      1      -0.39   
>      
> 7         F6      1    PF6     F6      1      -0.39   
> 
> [ constraints ]
> ;  ai    aj 
> funct       b0
>     1     
> 2     1   0.1560	; bond length = 
> 0.1560 nm
>     1     
> 3     1   0.1560
>     1     
> 4     1   0.1560
>     1     
> 5     1   0.1560
>     1     
> 6     1   0.1560
>     1     
> 7     1   0.1560
>     2     
> 3     2   0.22061731573	; 
> sqrt(2)*0.1560 nm
>     4     
> 5     2   0.22061731573
>     6     
> 7     2   0.22061731573
>     3     
> 4     2   0.22061731573
>     5     
> 6     2   0.22061731573
>     2     
> 7     2   0.22061731573
>     2     
> 4     2   0.22061731573
>     2     
> 6     2   0.22061731573
>     3     
> 5     2   0.22061731573
>     3     
> 7     2   0.22061731573
>     4     
> 6     2   0.22061731573
>     5     
> 7     2   0.22061731573
>     2     
> 5     2   0.3120	; 2*0.1560 nm
>     3     
> 6     2   0.3120
>     4     
> 7     2   0.3120
> -----------------------------------------------------------------
> -
> After minimizing the configuration, I got the confout.gro file as
> follows.
> -----------------------------------------------------------------
> -
> PF6
>     7
>     1PF6     
> P1    1   0.000   
> 0.000   0.000
>     1PF6     
> F1    2-592.510   0.000   0.000
>     1PF6     
> F2    3   0.000-592.510   0.000
>     1PF6     
> F3    4   0.000   0.000-592.510
>     1PF6     
> F4    5 592.510   0.000   0.000
>     1PF6     
> F5    6   0.000 592.510   0.000
>     1PF6     
> F6    7   0.000   0.000 592.510
>    2.50000   2.50000   2.50000
> 
> -----------------------------------------------------------------
> -
> 
> When I ran a simulation with md integrator option, it shows several
> messages as follows, and finally all the atoms go to infinity.
> 
> -----------------------------------------------------------------
> -
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 105.918804, max 105.972168 (between atoms 1 and 6)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, 
> constraint length
>       1      
> 2  180.0    0.1560  
> 16.6815      0.1560
>       1      
> 3  180.0    0.1560  
> 16.6710      0.1560
>       1      
> 4  180.0    0.1560  
> 16.6800      0.1560
>       1      
> 5  180.0    0.1560  
> 16.6772      0.1560
>       1      
> 6  180.0    0.1560  
> 16.6877      0.1560
>       1      
> 7  180.0    0.1560  
> 16.6787      0.1560
>       2      
> 3  180.0    0.2206  
> 23.5848      0.2206
>       4      
> 5  180.0    0.2206  
> 23.5873      0.2206
>       6      
> 7  180.0    0.2206  
> 23.5923      0.2206
>       3      
> 4  180.0    0.2206  
> 23.5840      0.2206
>       5      
> 6    nan    0.2206  
> 23.5915      0.2206
>       2      
> 7  180.0    0.2206  
> 23.5890      0.2206
>       2      
> 4  180.0    0.2206  
> 23.5897      0.2206
>       2      
> 6  180.0    0.2206  
> 23.5939      0.2206
>       3      
> 5  180.0    0.2206  
> 23.5824      0.2206
>       3      
> 7  180.0    0.2206  
> 23.5832      0.2206
>       4      
> 6  180.0    0.2206  
> 23.5931      0.2206
>       5      
> 7  180.0    0.2206  
> 23.5866      0.2206
> Wrote pdb files with previous and current coordinates
> -----------------------------------------------------------------
> -
> 
> What's wrong with my input files?
> 
> -- 
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