Hi Gmxers, I am doing a protein NMA with the mdp file like,
=========================================== define = -DEFLEXIBLE constraints = none integrator = nm ; emtol = 0.00001 emstep = 0.1 nsteps = 4000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 0 ; Frequency to update the neighbor list and long range forces ns_type = simple ; Method to determine neighbor list (simple, grid) ;vdwtype = switch vdwtype = cut-off rlist = 0.0 ; Cut-off for making neighbor list (short range forces) ;coulombtype = PME-switch ; Treatment of long range electrostatic interactions coulombtype = cut-off ;rcoulomb = 1.2 ; Short-range electrostatic cut-off rcoulomb = 0.0 ;rvdw = 1.2 ; Short-range Van der Waals cut-off rvdw = 0.0 pme_order = 4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 optimize_fft = yes pbc = no ===================================================== However, it shows "Fatal error: Constraints present with Normal Mode Analysis, this combination is not supported" Since I put "Constaints" none, I really do not get it. Can someone help me? thanks, Yao -- 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