[gmx-users] pull code problem: between protofilaments

[Shilpi Chaurasia]

Dear Gmx users,

I am 
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. 

I have 
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?  

Thanks,

best regards,
Shilpi Chaurasia
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