[gmx-users] COM motion removal problem

[Filip Ryjácek]

Hi all,
I have got serious problem with my simulation (DNA with counterions solvated 
in box of water). With the following settings GROMACS removed  C.O.M. motion 
periodically, but...it looks strange. Every 10ps the total temperature falls 
to 150K, but in 10ps is back again at 300K. See enclosed graphs (pdf 
format).
I know molecules should diffuse, but the fluctuations in temperature seem 
unnatural.

;
comm_grps           =  DNA Na+ SOL
nstcomm             =  10000 10000 10000
comm_mode           =  Linear
;


Thanks for help in advance
Filip



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