[gmx-users] pulling code

[Adam Herbst]

Hi all,
I am trying to measure the energy curve of unwinding the SNARE protein
complex.  This requires pulling the C-termini of two helices apart from each
other, while fixing certain other parts of the complex.  To do this I
excluded the reference group, so that all groups were pulled to absolute
coordinates.  However, as the protein was centered in the box, and because
the box center is where the coordinates transition from -boxlength/2 to
+boxlength/2 when using pbc (ie. the dateline), every time a group passes
through the center of the box in any of the 3 dimensions, it is suddenly
yanked violently through the box because it thinks it is now a full
boxlength away from its destination.  I modified the pull code to take the
shortest vector between the current position and destination, which seems to
fix this problem.  I also modified g_wham so that it can take the difference
between two groups' positions as the energy curve coordinate (since several
groups need to be fixed, neither of these two groups can be used as the
reference group).  However, as I use pressure coupling, the box dimensions
change during the simulation, and if one group has a positive and the other
a negative coordinate because they straddle the center of the box, the box
dimensions must be known at each timestep to get their actual separation.
 Is there an easier way to handle this type of simulation?  I don't think I
want to freeze or restrain the groups that need to be fixed, because they
must still be allowed flexibility to twist and deform--I only want to
roughly fix their centers of mass.  Any suggestions would be appreciated,

Thanks,

Adam
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