Hi, Initially, the pull group center of mass is at 8.16 nm and i want to pull 15 nm. I started with a box size of 37 nm in the pull direction.
The problem occurs when the COM is at 18.5 nm (ie at half the box length). Thanks for the attention. Amit On Mon, Jan 17, 2011 at 11:40 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Amit Choubey wrote: > >> Hi all, >> >> I am trying to do pulling simulation. Following are the pull parameters >> >> pull = umbrella >> pull_geometry = direction >> pull_vec1 = 0 0 1 >> pull_group1 = RNA >> pull_rate1 = 0.01 >> pull_k1 = 1000 >> pull_start = yes >> >> Everything works fine until the pull group COM reaches half the box >> length. The COM position changes by the box length and that causes huge >> force on the group. What should i do to fix this ? Also i am using NPT >> coupling. >> >> > You have to use a sufficiently large box, otherwise the periodic distance > becomes the reference distance when this happens. This has been discussed > numerous times on the list (hint: there is an archive for a reason!) and in > the tutorial linked here: > > > http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling > > -Justin > > Amit >> >> > -- > ======================================== > > 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 > > ======================================== > -- > 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 >
-- 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
