[gmx-users] potential
Dear all, I run 3 trajectory with an electric field of 1) E-z= 1 0.5 1 2) E-z= 1 2 1 3) E-z= 1 4 1 but the graphics of the potential of the system (gmx potential), gives a differential of potential of 1) -5V 2) -3V 3) -2,5 My system is a bilayer with a protein, plus water. ¿Why those differential of potential? thanks all -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Consult
Dear all, In one 300ns membrane simulation with water, in a box of 4x4x9 nn3. Which thermostat would you use and why? V-rscale or nose-hoover? thanks to all -- *Dr. Álvaro Ruiz * *Physicochemical Molecular LaboratoryDepartamento de QuímicaFacultad de CienciasUniversidad de Chile*Mobile: +56-9-51178101 Office: +56-2-9787443 arr...@ug.uchile.cl -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Equilibration
Dear users, I need to demonstrate that my box is in equilibrium. What is the maximum slope of the energy or the volume in function of time to demosntrate it? . Or exist anothe parameter to follow. Thank you very much. -- *Dr. Álvaro Ruiz * *Physicochemical Molecular LaboratoryDepartamento de QuímicaFacultad de CienciasUniversidad de Chile*Mobile: +56-9-51178101 Office: +56-2-9787443 arr...@ug.uchile.cl -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Distance between centers of mass
Dear GROMACS users: How can I calculate the distance between centers of mass of two residues in time with gmx distance?, I do not understand the sentence "com of resname AAA plus com of resname BBB" from the manual, pag 241 . Thanks. -- *Dr. Álvaro Ruiz * *Physicochemical Molecular LaboratoryDepartamento de QuímicaFacultad de CienciasUniversidad de Chile*Mobile: +56-9-51178101 Office: +56-2-9787443 arr...@ug.uchile.cl -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] question
Dear gromacs users: I need to build a phospholipid bilayer, but for some reason it gets water, I think the problem could be solved with the construction of a plane that prevents the passage of water molecules. In short, can GROMACS generate a plane that prevents the passage of one type of molecules?. Thank you very much. -- *Álvaro Rodrigo Ruiz Fernández Laboratorio Fisicoquimica MolecularDepartamento de QuímicaFacultad de CienciasUniversidad de Chile*Mobile: +56-9-75643659 Office: +56-2-9787443 arr...@ug.uchile.cl -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] question
Dear gromacs users: How I can multiply a box full of molecules from 1x1 to 2x2 ?, I know I can use Avogadro but in this case it does not work, I think for the periodic boundary conditions. Thank you very much -- *Álvaro Rodrigo Ruiz Fernández Laboratorio Fisicoquimica MolecularDepartamento de QuímicaFacultad de CienciasUniversidad de Chile*Mobile: +56-9-75643659 Office: +56-2-9787443 arr...@ug.uchile.cl -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] question
Dear gromacs users: How I can multiply a box full of molecules from 1x1 to 2x2 ?, I know I can use Avogadro but in this case it does not work, I think for the periodic boundary conditions. Thank you very much -- *Álvaro Rodrigo Ruiz Fernández Laboratorio Fisicoquimica MolecularDepartamento de QuímicaFacultad de CienciasUniversidad de Chile*Mobile: +56-9-75643659 Office: +56-2-9787443 arr...@ug.uchile.cl -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
