[gmx-users] Parallel pulling with Gromacs 4.0.7: COMM mode problem

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue Mar 30 15:11:04 CEST 2010

> If you pull in G3 with AFM option, with your reference groups is the  
> surface, in the output pull.pdo file what you will get is  solute  
> (pulled group) coordinates /wrt the surface...

Yes. Can we see the data that you get as output in each case and tell  
us what the major difference is?

> the coordinates of your reference groups as a function of time does  
> not change, right...

Not normally true. A pulling force will be applied to your surface in  
addition to your solute. The only thing that might keep it static is:

> Note that I have angular COMM mode for such simulation.
> comm_mode                = angular
> nstcomm                  = 1
> comm_grps                = DIAM

But who knows how and if this works in gromacs 4 with domain  
decomposition. Please try gromacs 4 in serial and see if you get the  
same unexpected results.

> that the output coordinates for my pulled groups should be /wrt the  
> surface (DIAM) However, the situation is completely, how can I say,  
> smtg else...

Can you show some data for this?

> however, it treats like iit_grps is 0 0 0 all the time but it is not

Can you show some data for this?

> In the log file, I can see that COMM grp is the surface and the pulling
> is /wrt the surface again but the output gives smtg as COMM grp is  
> the whole box

Can you show some data for this?

Also, please use entire words. smtg and /wrt, while quicker to type,  
are actually harder and more annoying to read.

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