I am coming across the similar problem. In my case I was using semiisotropic pressure and set the compressiblity in x/y as 0.0 to construct the NPAT ensemble. The area in xy plane is not changing but the dimension of z has changed. The system behaves well without the application of electric field of strength 0.5 V/nm. However, the lipid molecules rapidly penetrate (within 5ns period) into the water in presence of that electric field (I think it is rapid electroporation). Basically, after a while it is like a mixture of lipid and water system and the bilayer has destroyed. I don't understand how much logical is it?
These are my keywords Pcoupl = berendsen Pcoupltype = semiisotropic tau_p = 5.0 5.0 compressibility = 0.0 3e-4 ref_p = 1.0 1.0 ;Electric fileld E-z = 1 0.5 0 On Mon, Aug 19, 2013 at 8:22 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/18/13 11:21 PM, udels can wrote: > >> Hi All, >> >> I am facing a strange problem when I was trying to apply electric field >> across a membrane, DMPC, water and ion system. To apply electric field >> across the membrane (in +ve z direction), I had used NPzAT ensemble, where >> the Pz is the constant pressure along the z direction and A is the >> constant >> area in xy plane. The following essential keywords were used to construct >> such kind of system. >> >> Pcoupltype = anisotropic >> tau_p = 1.0 1.0 >> compressibility = 0.0 0.0 3e-4 0.0 0.0 0.0 >> ref_p = 0.0 0.0 1.0 0.0 0.0 0.0 >> >> ;Electric fileld >> E-z = 1 2.0 0 >> >> Here, I had chosen anisotropic coupling and two tau_ps are for two >> groups(DMPC and water_ion). The compressibility for x, y and off diagonal >> elements were chosen as 0 and the compressibility in z direction was >> chosen >> as 3e-4. Logically, such compressibility factors ensures that area in xy >> plane will not change. >> >> However, I am not getting the expected results. The strange thing is that >> the bilayer and water mixed up, the lengths of box abruptly are changed in >> three directions, and the water molecules are arranged in a linear >> fashion >> (I think it is due to the effect of electric field). May be the electric >> field is high enough and as a result the electroporation occurs very >> rapidly. Moreover, the are area in xy plane is not fixed, they are >> changing >> abruptly. I don't understand why does it happen. This is because the >> compressibilities are zero along x and y directions. Another strange thing >> is that there are too many LINCS warning. How do I resolve this issue. >> Please help me out in this regard. >> >> > Does a simulation in the absence of the electric field run normally? It > sounds like there is something fundamentally wrong, but with so much going > on it's hard to determine the root cause. > > -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 * 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
