[gmx-users] pull code problem: between protofilaments
shilpi.chaurasia at unimi.it
Thu Sep 29 18:00:05 CEST 2011
Dear Gmx users,
studying the interaction between the tubulin protofilaments arranged
in parallel. For this operation, I have considered a tetramer and a dimer from two protofilaments
respectively (say PRO-1 and PRO-2), tetramer in PRO-1 and a dimer in
PRO-2. I want to
move the dimer of PRO-2 over the tetramer of PRO-1 along the length of
protofilaments in one axis only, keeping the PRO-1 fixed to its original
position. I tried by assuming tetramer as 'reference group' and the
dimer as 'pull group' in pull code but the system crashed.
succeeded in separating two dimers in Z-axis by using
'distance' geometry. But this case is quite different, as the pulling is
not face-to-face but rather a sliding movement over another
protofilament. Here, the COM distance between the pull group (dimer of
PRO-2) and reference group (tetramer of PRO-1) first decreases and then increases while it moves. How can I simulate this operation by using pull code?
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