Dear friends, when trying to run a double precision vanilla MD, version 4.5.1, with a small hairpin molecule (248 atoms) in implicit solvent (generalized Born approximation) this is what I get:
--------------------------------------------------------------------------------------------- Getting Loaded... Reading file hairpin-md-gb-1.tpr, VERSION 4.5.1 (double precision) Loaded with Money starting mdrun 'Protein' 50000 steps, 50.0 ps. Segmentation fault --------------------------------------------------------------------------------------------- In some trials, I also get a message about the distance in an 1-4 interaction being beyond the table size, but this is not the case. Strangely enough, the MD runs fine with a development version (4.0.99, downloaded from the GIT repository). I am attaching my mdp and pdb files. Regards Silvio a Beccara Dip. di Fisica - Universita` di Trento 14 Via Sommarive 38123 Povo - TN tel: 0461-881631
; ; Molecular dynamics thermostatted @ 1600.0 K ; cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = md comm_mode = angular nsteps = 50000 dt = 0.001 pbc = no periodic_molecules = no nstcomm = 10 nstxout = 10 ; nstfout = 1 ns_type = simple rlist = 2.0 rcoulomb = 2.0 rvdw = 2.0 coulombtype = cut-off vdwtype = cut-off ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Nose-Hoover temperature coupling is on in one group Tcoupl = nose-hoover tau_t = 0.3 tc-grps = protein ; Generate velocites is on at 1600.0 K. gen_vel = yes ref_t = 1600.0 gen_seed = 312500933 ; no barostat Pcoupl = no ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = gbsa ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = obc ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 2.0 ; Dielectric coefficient of the implicit solvent gb_epsilon_solvent = 78.3 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 gb_dielectric_offset = 0.009 sa_algorithm = still ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA ; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2. sa_surface_tension = 2.092
ratch-frame63.pdb
Description: application/vnd.palm
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