[gmx-users] pull code problem: between protofilaments

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sun Oct 2 15:43:44 CEST 2011

Dear Shilpi:

Can you use something like this?

pull                     = umbrella
pull_geometry            = position
pull_dim                 = N N Y
pull_vec1                = 0 0 0
pull_start               = no
pull_ngroups             = 1
pull_group0              = PRO-1
pull_pbcatom0            = <set this or use 0>
pull_group1              = PRO-2
pull_pbcatom1            = <set this or use 0>
pull_init1               = 0 0 <set initial value here for z-axis>
pull_rate1               = 0
pull_k1                  = 500.0
pull_nstxout             = 500
pull_nstfout             = 500

The above is for umbrella sampling. If you want to do continuous  
pulling, then:

pull_start               = yes
pull_rate1               = <set the rate>

### Also:

Next time you post, please provide more specifics. For example, I  
suggested a .mdp file in specifics to you above and I bet it would  
have been harder for you to guess what I meant if I had just told you  
the general idea instead of pasting some .mdp options. Likewise, your  
initial post would have been clearer it you had copied and pasted the  
.mdp pull code section that you tried to use.


-- original message --

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?


best regards,
Shilpi Chaurasia

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