[gmx-users] absolute reference for pulling and center of mass removal

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Oct 27 14:49:43 CEST 2010


instead of directly answering your question, let me suggest that you  
don't want to pull in absolute coordinates. Probably, you want to pull  
your polymer with respect to the position of some other (non-water)  
reference group. The only reason that I can think of to use absolute  
coordinates it a) testing or b) you really want to simulate  
non-equilibrium (but perhaps steady state) flow properties like  
turbulence. In the latter case, you can probably use constant force  
pulling and ignore the warning.

If you're thinking of something else, please tell us what you want to achieve.


Dear gmx-users?

I intend to pull a polymer in the bulk water using the pull code in
gmx4. When I checked the manual, it was said " With an absolute
reference the system is no longer translation invariant and one should
think about what to do with the center of mass motion." Yes, I set the
pull group with the polymer and the reference group with the default
(0,0,0). Then I received a warning after grompp as follows:
"You are using an absolute reference for pulling, but the rest of the
system does not have an absolute reference. This will lead to

I am not sure about the artifacts artifacts, could somebody give me a
more definite explanation.

Assuming we pull the COM of the polymer along x, and then the COM of
water in x is coupled with that of the polymer, but the COM of water
in yz is uncoupled. As a result, the momentum of system in yz could be
nonzero for long time simulations if no COM removal is applied in yz.
So to speak, if we do not remove the COM motion, artifacets could be
induced by round errors in uncoupled yz direction. Am I right?

How the deal with the COM removal in this case?

I have done two tests here:

1) Set comm-grps = system. The polymer and the water flowed in the
negative direction.
2) Set comm-grps = polymer SOL. The polymer still moved in x, and no
COM motion observed for SOL.

Which one could be appropriate, and if both are not ok, is there a way
to solve the problems? Thanks for your suggestions in advance!

Best regards,

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