[gmx-users] Does afm influence other groups?

Robert Vacha vachr9am at port.kolej.mff.cuni.cz
Wed Jan 14 20:14:01 CET 2004

Hi Anton,

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.
Robert Vacha

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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