[gmx-users] Does afm influence other groups?
vachr9am at port.kolej.mff.cuni.cz
Wed Jan 14 20:14:01 CET 2004
thank you for your note.
I tried to do the experiment in a way you advised me, but unfortunatelly it doest't work - no matter when
using removal of center of mass motion (nstcomm) or not.
But still thank you for your advice.
Tuesday, January 13, 2004, 7:58:55 PM, you wrote:
AF> 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.
AF> Do you use removal of center of mass motion (nstcomm)? That may cause
AF> the 'stationary' atoms to move in the opposite direction to the 'pulled'
AF> atoms. Note, I don't use AFM, this is just an educated guess from my
AF> knowledge of Gromacs' entrails.
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