[gmx-users] Does afm influence other groups?
feenstra at chem.vu.nl
Wed Jan 14 13:58:07 CET 2004
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.
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| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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