@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. 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