How about applying position restarints with a strong force constant? What is less computationally expensive: position restrained, freezing the whole molecule? The nanotube should be rigid... Shall I place the edged of the tube on the box edge as well and use pbc=xyz and periodic molecules = yes?
Thanks, Steven On Thu, Sep 26, 2013 at 9:28 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/26/13 12:05 PM, Dr. Vitaly Chaban wrote: > >> Steven - >> >> I would use a simple harmonic bond. >> >> > Note that either in the case of the distance restraint or harmonic > interaction approach, both the CNT and the molecule to which it is tethered > need to be in the same [moleculetype], so run pdb2gmx (or whatever you are > using) with care. > > -Justin > > > >> Dr. Vitaly V. Chaban >> >> >> On Thu, Sep 26, 2013 at 5:12 PM, Steven Neumann <s.neuman...@gmail.com> >> wrote: >> >>> Thank you for this. And also I wish to attach a chain to my nanotube so >>> they >>> will be both able to move together. Is that a matter of distance >>> restraints >>> between nanotube atom and first atom of my chain or again - LINCS? Both >>> chain and nanotube are made of the same type of 8 type of atoms. Please, >>> advise. >>> >>> Steven >>> >>> >>> On Thu, Sep 26, 2013 at 3:19 PM, Dr. Vitaly Chaban <vvcha...@gmail.com> >>> wrote: >>> >>>> >>>> I am just curious why the system would explode without >>>> "periodic_molecules = yes". If the PBC procedure is applied before >>>> harmonic bond potential is calculated, than the opposite nanotube >>>> atoms should be (already) seen as neighboring. This looks the same as >>>> the solvent molecule, one atom of which crossed the box boundary. >>>> >>>> No? >>>> >>>> >>>> >>>> Dr. Vitaly V. Chaban >>>> >>>> >>>> On Thu, Sep 26, 2013 at 3:59 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>>> >>>>> >>>>> >>>>> On 9/26/13 8:39 AM, Steven Neumann wrote: >>>>> >>>>>> >>>>>> Dear Gmx Users, >>>>>> >>>>>> I have my carbon nanotube and I wish to make it infinite in lenght. >>>>>> Which >>>>>> mdp options whall be used? pbc = xy and z is the infinite dimension? >>>>>> another issue: Would you apply bonds between carbon atoms within the >>>>>> nanotube or constraints using LINCS? Which of them is less >>>>>> computationally >>>>>> expensive for the run? >>>>>> >>>>>> >>>>> Use "pbc = xyz" in conjunction with "periodic_molecules = yes" >>>>> otherwise >>>>> the >>>>> topology gets messed up trying to form unreasonable bonds. The >>>>> periodic_molecules keyword in the .mdp allows for bonds to be >>>>> maintained >>>>> over PBC. >>>>> >>>>> I remember a very old post somewhere in the archive that said one >>>>> should >>>>> not >>>>> apply pressure coupling along the axis of the nanotube, due to some >>>>> difficulties with maintaining the bonded geometry, but since I have >>>>> never >>>>> done CNT simulations, take the fact that I'm just repeating what I've >>>>> heard >>>>> for what it's worth :) >>>>> >>>>> Constraints always come with the cost of communication, so I would >>>>> imagine >>>>> harmonic bonds are "less expensive." I really don't see constraints as >>>>> a >>>>> limiting factor for performance, though. >>>>> >>>>> -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<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<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? 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