[gmx-users] the broken of the molecules

[Mark Abraham]

Hi,

If you are using PBC, mdrun will sometimes write sets of coordinates such that molecules appear "broken" across periodic boundaries. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions for solution approaches.

Linear species can sometimes have other problems, which have been discussed on the mailing list before.

Mark

----- Original Message -----
From: kecy_wu at sina.com
Date: Monday, September 6, 2010 18:43
Subject: [gmx-users] the broken of the molecules
To: gmx-users <gmx-users at gromacs.org>


>  Hello, I do the energy minimization of the butylene box , but some butylene molecules are broken after that. The butylene itp file is produced by PRODRG, as follows:
 
>  
 
> [ moleculetype ]
> ; Name nrexcl
> BUT      3
 
> [ atoms ]
> ;   nr      type  resnr resid  atom  cgnr   charge     mass
>      1       CH3     1  BUT      C9     1    0.0049   15.0350   
>      2       CH2     1  BUT      C6     1   -0.02442  14.0270   
>      3         C     1  BUT      C3     1    0.07957  13.0190   
>      4         C     1  BUT      C2     1   -0.06005  14.0270   
 
> [ bonds ]
> ; ai  aj  fu    c0, c1, ...
>    2   1   2    0.155   7150000.0    0.155   7150000.0 ;    C6   C9   
>    2   3   2    0.153   7150000.0    0.153   7150000.0 ;    C6   C3   
>    3   4   2    0.135   7150000.0    0.135   7150000.0 ;    C3   C2   
 
> [ pairs ]
> ; ai  aj  fu    c0, c1, ...
>    1   4   1                                           ;    C9   C2   
 
> [ angles ]
> ; ai  aj  ak  fu    c0, c1, ...
>    1   2   3   2    112.5       520.0    112.5       520.0 ;    C9   C6   C3   
>    2   3   4   2    125.0       610.0    125.0       610.0 ;    C6   C3   C2   
 
> [ dihedrals ]
> ; ai  aj  ak  al  fu    c0, c1, m, ...
>    1   2   3   4   1      0.0    1.0 6      0.0    1.0 6 ; dih    C9   C6   C3   C2 
 
>  
 
> Can  you show me why the butylene molecules would  be broken?
 
> Thank you very much !
 
>  
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