Dear gmx-users, I am trying to perform the Normal Mode Analysis of 24 kDa protein in water. Here is the .mdp file I am using:
integrator = nm dt = 0.002 nsteps = 10000 emtol = 1 nstcomm = 1 nstxout = 0 nstxtcout = 1000 nstvout = 0 nstlog = 5000 nstenergy = 20 nstlist = 6 ns_type = grid coulombtype = cut-off epsilon_r = 80.0 rcoulomb = 1.4 fourierspacing = 0.12 pmeorder = 4 optimize_fft = yes ewald_rtol = 1.0e-5 DispCorr = EnerPres constraints = none rlist = 0.9 rvdw = 0.9 Tcoupl = berendsen ref_t = 330 tc-grps = protein tau_t = 0.5 Pcoupl = no Pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = no gen_temp = 300 gen_seed = 1993 And I get the error message: Fatal error: Constraints present with Normal Mode Analysis, this combination is not supported For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors despite the constraint = none line. I am using GROMACS 4.5.4 Any suggestions will be very welcomed Thanks! -- Andrey Dyachenko PhD Student Design, structure and synthesis of peptides and proteins Institute for Research in Biomedicine (IRB Barcelona) C/Baldiri i Reixac 10-12 08028 Barcelona Tel: +34 93 403 71 27 Fax: +34 93 403 71 26 www.irbbarcelona.org www.pcb.ub.es/giralt/html/home.html
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