[gmx-users] crossing angle value
dear all i use g_bundle to calculate the crossing angle, but i do not know how to define the positive or negative value by left hand or right hand angle. someone could tell me how to define? Cao Ph.D Nankai University Tianjin China -- 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 about g_bundle
dear all i want calculate crossing angle of two helix in membrane, and use g_bundle. but the -na command i do not know what the exact mean. how could i define the -na for calculate the crossing angle of two helix at X-axis? thanks a lot. Cao -- 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] combine two solvent box to one large box.
hello all I have made two solvent boxes with DIFFERENT protein in each box, the box have the same X-Y-Z length. I want to combine two boxes to one large box at one dimension like X or Y Witch command could do that?? best regard Cao, PhD Institute of Physics Nankai University Tianjin, China -- 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] double size a box
dear all i want to study two proteins interaction in membrane protein. i have embed a protein in the membrane and added water to form a cubic box, and i want double in size by repeating the box to get a rectangular box with two proteins. so ,which command in gromacs could do that automaticly? best regard Cao Ph.D Nankai university, China -- 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] a question about Electric fields
hello all I have some questions about add a voltage to a membrane with a protein system 1, how could i add a such as 30mv Electric fields in Z-axis(along the pore) 2, i used the Electric fields in mdp file to define Electric fields(E-z,0.03mv/nm) in z-axis but the subunit(five subunits in a protein) are move along the direction of Electric fields to another membrane(pbc. xyz) one by one( the whole protein could not stay here), why? how could i solve this problem? best regard Cao Ph.D Nankai University, Tianjin, China -- 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.
