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. Thanks in advance shen -- 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
