Oh, thanks! On Thu, Oct 6, 2011 at 7:59 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Sai Janani Ganesan wrote: > >> 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? >> >> > When setting "distance" as the pull_geometry, only pull_dim is used; > pull_vec is ignored. If you want to define vectors, use the "direction" > pull_geometry. > > -Justin > > Thanks, >> Sai >> >> >> >> >> On Thu, Oct 6, 2011 at 9:14 AM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> 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 <http://vt.edu> | (540) 231-9080 >> <tel:%28540%29%20231-9080> >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <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 >> <mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> >> <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> >> >> >> <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 >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> <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/ >> > > -- > ==============================**========== > > 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*
-- 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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
