Hi, Thanks for the reply!
I tried the rates, and only the terminal with positive rate gets pulled. The first and the last amino acids are spatially oriented one behind the other. I think defining a vector might work better, but I am not sure why nothing happens when I define a pull_vec1 and pull_vec2. Am I missing anything? Thanks, Sai On Thu, Oct 6, 2011 at 9:14 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Sai Janani Ganesan wrote: > >> Hi, >> >> I am trying to pull the first from the last amino acid of a protein to >> completely unfold the protein in the X direction. I chose the middle amino >> acid as the reference, and the groups get pulled in the same direction or >> opposite direction (which is what I want) depending on the trial. I am >> trying to find a definite method to completely unfold it. >> I define a different vector (pull_vec1 and pull_vec2) with +x and -x >> values and that does not even pull the protein >> I tried using only pull_group1 and pull_group2, without a reference, and >> neither groups get pulled. >> I chose different references, I do have some success but I don't think it >> is the best way to do it. >> >> How do I pull the N and C terminal apart, by simultaneously pulling them >> in opposite directions?Why is my vector definition wrong? >> >> This is my pull code: >> >> pull = umbrella >> pull_geometry = distance >> pull_dim = Y N N >> pull_start = yes pull_ngroups = 2 >> pull_group0 = Chain-C >> pull_group1 = Chain-B >> pull_group2 = Chain-A >> >> %pull_vec1 = -31 0 0 >> %pull_vec2 = 31 0 0 >> > > I suspect the % signs will mess things up, but probably will give a fatal > error, if nothing else. > > > pull_rate1 = 0.002 pull_k1 = 1000 pull_rate2 = >> 0.002 pull_k2 = 1000 >> > > Here's the problem. You're telling the two pulled groups to move in the > same direction. With "distance" geometry, the selections are a bit more > simplistic. If you set pull_rate1 to -0.002 and pull_rate2 to 0.002, the > groups will be pulled in opposite directions. Otherwise, you're just towing > your protein along in the box. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- *"Every sentence I utter must be understood not as an affirmation but as a question." - Niels Bohr*
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