I want to come back to the question of the NMA in the Gromacs :) I've found in manual possible algorithms of this analysis- I must calculate Hessian matrix via Md-run and then calculate modes with g_nmens program
1- I've performed CG minimization of my initianl structure 2- I've loadet to the gromp .tpr file of my minimized structure 3- I've used mdrun and obtain error Fatal error: Constraints present with Normal Mode Analysis, this combination is not supported So I suppose that the problem with my .mdp file wich consist of the parametres for the NMA of Lyzosyme in water :) integrator = nm ; Normal Mode Analysis ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; Short-range electrostatic cut-off rvdw = 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) How I should edit this configure file for my NMA? If I edit the above parametries for rvdw etc in accardance to the http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis?highlight=nmI've obtained error that ERROR 1 [file nma.mdp]: With coulombtype = PME, rcoulomb must be equal to rlist If you want optimal energy conservation or exact integration use PME-Switch ERROR 2 [file nma.mdp]: With vdwtype = Cut-off, rvdw must be >= rlist What are the most suitable coulombtype for the NMA and combination of the other options? James
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
