Hi all;I am an amateur gromacs user, but i have read all the tutorials i could find on how to perform md simulations using gromacs, however i still cant find any tutorial about how to include orientation restraints in my simulations. i want to perform a simulation on a helical protein and include 4 types of RDC data from two experiments. In the manual their is an example with N-H RDC data, however i need the constant ci for other types of RDC's ( C-N, C-H, Calpha-Halpha) does anybody know how to calculate them or where can i find them? also this is an example of the itp file that contains my RDC value:[ orientation_restraints ] ; ai aj type exp. label alpha const. obs. weight ; Hz nm^3 Hz Hz^-2 ;residue 2 20 21 1 1 1 3 6.083 7.72483 1.0 20 21 1 2 2 3 6.083 7.27571 1.0 ;residue 4 46 47 1 1 3 3 6.083 1.864475 1.0 46 47 1 2 4 3 6.083 -14.2043 1.0 ;residue 5 66 67 1 1 5 3 6.083 10.16845 1.0 66 67 1 2 6 3 6.083 -11.278 1.0 and in the topology file i added this: ; Include 1a1z protein topology #include "1a1z.itp"
; Include Orientation restraint file #ifdef POSRES #include "ocNH.itp" #endif and then in my mdp files for the minimization, equiliberation and md i have this: define = -DPOSRES ; restrain the protein are these steps correct ??????thank you for your helpHanin Omar -- 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.
