Does anyone have proper parameters for CNTs ? I have been trying to perform Simulations with finite CNTs. However, none of the parameters so far (obtained from literature) seem to give the output temperatures equal to set temperatures.
I have been looked into my input files time and again, but I could not locate any bug so far. The problem is if I simulate my CNT with bonds angles dihedrals and 1-4 interactions and constraint the bonds, the temperature of the CNT seems to deviate far from the set temperature with reasonable values of tau-t using the sd integrator in GROMACS. Does anyone have parameters for CNTs such that they work with the SD integrator with reasonable tau-t values? On Tue, Sep 17, 2013 at 5:14 PM, HANNIBAL LECTER <hanniballecte...@gmail.com > wrote: > @Vitaly. Yes you are right. However, I noticed that if I do not constraint > the bonds in my CNT my simulations run fine. It is indeed surprising to me > but I do not have much experience with simulating CNTs and if not > constraining the bonds seem to get things done, I think it is a viable > option. But still need to test a lot of things before I can decide on the > final settings. > > > On Tue, Sep 17, 2013 at 5:11 PM, HANNIBAL LECTER < > hanniballecte...@gmail.com> wrote: > >> Yes. That is the way to go about it. I was hoping for a more lazy >> approach... Thanks anyways. >> >> >> On Tue, Sep 17, 2013 at 5:07 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >>> >>> >>> On 9/17/13 4:50 PM, HANNIBAL LECTER wrote: >>> >>>> Is there a smart way of writing the constraint sections in the topology >>>> file other than entering the values manually ? >>>> >>>> >>> Write a script that parses the [bonds] directive of the post-processed >>> topology (output by grompp -pp) and write the relevant fields to a >>> [constraints] directive. >>> >>> -Justin >>> >>> >>> >>>> On Tue, Sep 17, 2013 at 10:10 AM, rahul seth >>>> <rahul.seth.grom...@gmail.com>**wrote: >>>> >>>> Thanks >>>>> >>>>> >>>>> On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul <jalem...@vt.edu> >>>>> wrote: >>>>> >>>>> >>>>>> >>>>>> On 9/17/13 10:00 AM, HANNIBAL LECTER wrote: >>>>>> >>>>>> Is there a way to constraint bonds of a part of the system while >>>>>>> keeping >>>>>>> the other part flexible? For example for a simulation with two >>>>>>> >>>>>> proteins, I >>>>> >>>>>> would like to constraint the bonds of one and would like to keep the >>>>>>> >>>>>> other >>>>> >>>>>> flexible. >>>>>>> >>>>>>> I would prefer to use LINCS to constraint the system >>>>>>> >>>>>>> >>>>>>> Set the constraints explicitly in the topology of one protein using >>>>>> a >>>>>> [constraints] directive. Then set "constraints = none" in the .mdp >>>>>> file. >>>>>> The constraints read from the topology will override the .mdp >>>>>> setting >>>>>> while leaving all other bonds unconstrained. >>>>>> >>>>>> -Justin >>>>>> >>>>>> -- >>>>>> ==============================****==================== >>>>>> >>>>>> Justin A. Lemkul, Ph.D. >>>>>> Postdoctoral Fellow >>>>>> >>>>>> Department of Pharmaceutical Sciences >>>>>> School of Pharmacy >>>>>> Health Sciences Facility II, Room 601 >>>>>> University of Maryland, Baltimore >>>>>> 20 Penn St. >>>>>> Baltimore, MD 21201 >>>>>> >>>>>> jalemkul@outerbanks.umaryland.****edu <jalemkul@outerbanks.** >>>>>> umaryland.edu <jalem...@outerbanks.umaryland.edu>> >>>>>> >>>>> | (410) >>>>> >>>>>> 706-7441 >>>>>> >>>>>> ==============================****==================== >>>>>> >>>>>> -- >>>>>> gmx-users mailing list 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> >>>>> >**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> >>>>>> < >>>>>> >>>>> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>>>> > >>>>> >>>>>> >>>>>> -- >>>>> 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> >>>>> >>>>> >>> -- >>> ==============================**==================== >>> >>> >>> Justin A. Lemkul, Ph.D. >>> Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 601 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu>| >>> (410) >>> 706-7441 >>> >>> ==============================**==================== >>> >>> -- >>> 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> >>> >> >> > -- 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