[gmx-users] Does afm influence other groups?

[Anton Feenstra]

Robert Vacha wrote:

> Hi all,
>   Does connecting of two groups by "afm pull code" influence other groups or is there something wrong with my simulation?
>   I have a  simple simulation using AFM pull code in version 3.2.0beta and also 3.1.5_prep1. 
> My simulation consists of 4 atoms    
> 1SOL     KR    1   0.697   0.647  15.809   
> 2SOL     KR    2   0.697   0.647  15.282 
> 3DRG     AR    3   0.697   0.647  20.000
> 4DRG     AR    4   0.697   0.647  10.000 
> in normal NVE simulation withnout afm pull argons stay(cut off =1nm) and kryptons oscilate in Lennard-Jones potential. 
> But, if I connect my two argons by afm, the other group-kryptons- stays and does not move.

Do you use removal of center of mass motion (nstcomm)? That may cause
the 'stationary' atoms to move in the opposite direction to the 'pulled'
atoms. Note, I don't use AFM, this is just an educated guess from my
knowledge of Gromacs' entrails.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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