Dear Chris, 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.
regards, Shilpi On 02/10/11, chris.ne...@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. > > Chris. > > -- 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? > > Thanks, > > best regards, > Shilpi Chaurasia > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface or > send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >
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