[gmx-users] freeze dummy atom completely

Berk Hess gmx3 at hotmail.com
Mon Aug 16 11:19:55 CEST 2004

>My problem is that, if I look at snapshots, my dummy atom doesn't remain
>at its z-position, it gets pushed away.  I guess the problem
>might be the mass of the dummy, I tried making it 0 but then grompp warns:
>WARNING 1 [file "topol.top", line 2387]:
>   atom DUM (Res DUMM-1502) has mass 0
>and mdrun crashes on:
>Fatal error: ci = -2147483648 should be in 0 .. 431 [FILE nsgrid.c, LINE 
>mass -1 also doesn't help. Is there a definite solution to keep it at its 

This question has been answered before on the list.
Unfortunately the pull code ignores the freeze groups.
Therefore the dummy will just move according to the constraint force.
It would be nice to have this problem fixed, but there is a large
number of combinations of freeze and pull dimensions and maybe
also other things to consider.

In the meantime I think you can run the simulation by giving the dummy
a mass of 10e10 or 10e20.


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