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
