[gmx-users] pull code problem: between protofilaments
shilpi.chaurasia at unimi.it
Mon Oct 3 17:19:39 CEST 2011
Thank a lot for your reply. I am trying the pull code that you have suggested. And I would be more specific about the problem and code in my future mails.
On 02/10/11, chris.neale at utoronto.ca wrote:
> 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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