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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