Would there be artifacts because of that?
On Wed, Sep 11, 2013 at 9:20 AM, HANNIBAL LECTER <hanniballecte...@gmail.com > wrote: > Yes > > > On Wed, Sep 11, 2013 at 9:18 AM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 9/11/13 9:09 AM, HANNIBAL LECTER wrote: >> >>> 500ps simulations. Yes everything is immersed in a bath of water. Can you >>> please elaborate a little more as to why do you doubt semiisotropic >>> coupling may not be necessary? >>> >>> >> Water should compress isotropically. I understand where you're coming >> from, given that you have observed a seemingly semiisotropic compression of >> the system, but physically that is not right. Something like a membrane, >> that has properties that make it sensible to couple x-y and z compression >> separately, would use semiisotropic coupling. >> >> Is this a system in which you're using freezegrps? >> >> -Justin >> >> >>> On Wed, Sep 11, 2013 at 9:05 AM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>>> >>>> On 9/11/13 9:01 AM, HANNIBAL LECTER wrote: >>>> >>>> I am trying to simulate a peptide inside a nanotube and using isotropic >>>>> pressure coupling for the system. The nanotube is immersed in a >>>>> cuboidal >>>>> box of water and aligned along the z direction of the box. >>>>> >>>>> The XX, YY components of the stress tensor are about ~570 bars and the >>>>> ZZ >>>>> component is about -1179 yielding a total pressure of about 2 bars >>>>> whereas >>>>> my set pressure is ~1.01325 bars. Is this okay or should I be using >>>>> semiisotropic coupling? >>>>> >>>>> >>>>> Over how long a time period are these values? If everything is >>>> immersed >>>> in a bath of water, I doubt semiisotropic coupling is necessary. >>>> >>>> -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> >>>> <htt**p://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<h**ttp://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> >>>> > >>>> >>>> >> -- >> ==============================**==================== >> >> 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