It seems that i cannot figure out a way to change the absolute reference point (Its the origin by default).
Amit On Mon, Jan 17, 2011 at 5:52 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Amit Choubey wrote: > >> Yes Justin i understand that. Heres what i think is going on >> >> I dont have any reference group. Now the COM distance is calculated wrt >> the origin and whenever the COM is more than half of the box its causing >> problem. >> >> > Correct. > > > I think changing the absolute reference to the initial COM of the pull >> group (using pull_init1) should fix this issue but i am not confident. >> >> > Using a defined reference group is the better method. That way, the pull > distance is calculated with respect to this reference, and it sounds like > that will allow you to use the box you have already set up. > > -Justin > > Thanks for looking into this. >> >> On Mon, Jan 17, 2011 at 5:36 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Amit Choubey wrote: >> >> Hi, >> >> I am still not able to see the reason for the periodic distances >> coming into picture. >> >> >> I guess I don't fully understand your procedure. If you only want >> to pull to a COM separation of 15 nm, there should be no problem, >> but yet you're achieving a COM separation of 18.5 nm? That's >> exactly the problem. If your box is 37 nm, 18.5 nm corresponds to >> the transition at which the code utilizes either the unit cell >> distance or the periodic distance as the restraint distance. So it >> is as this point that your forces go haywire. >> >> -Justin >> >> 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 <mailto:kgp.a...@gmail.com> >> <mailto:kgp.a...@gmail.com <mailto: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 <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto: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 <http://vt.edu> <http://vt.edu> | >> >> (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list >> gmx-users@gromacs.org <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read >> http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> -- ======================================== >> >> 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 >> 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 >> 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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > 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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