Hi, I am still not able to see the reason for the periodic distances coming into picture.
Also, why pull_geometry = direction_periodic cannot be used with P-coupling; although it seems to do what i want. Amit On Mon, Jan 17, 2011 at 1:04 PM, Amit Choubey <kgp.a...@gmail.com> wrote: > 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 >> > >
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