Thank you for the tips! This is my .mdp file:
title = nacl ; Run parameters integrator = md ; leap-frog integrator nsteps = 2000000 ; 2 * 500000 = 1000 ps, 1 ns dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps ; Bond parameters continuation = no ; Restarting after NPT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.4 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.6 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = system ; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 335 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Berendsen;Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-6 ; isothermal compressibility of NaCl, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 335 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed energygrps = Na Cl MOL notattached Contents of index file index.ndx -------------------------------------------------- Nr. Group #Entries First Last 0 System 16800 1 16800 1 Ion 5600 1 5600 2 Na 2800 1 2800 3 Cl 2800 2801 5600 4 MOL 11200 5601 16800 5 Other 11200 5601 16800 6 Na 2800 1 2800 7 Cl 2800 2801 5600 8 MOL 11200 5601 16800 Contents of index file select.ndx -------------------------------------------------- Nr. Group #Entries First Last 0 notattached_0.000 3050 5901 16800 2014-03-26 16:36 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: > > > On 3/26/14, 11:30 AM, Josip Lovrić wrote: > >> Hello, >> >> I managed to create notattached group but now it is not recognizing system >> group when I compile it with gromp. >> I get this answer: >> >> Fatal error: >> Group system referenced in the .mdp file was not found in the index file. >> Group names must match either [moleculetype] names or custom index group >> names, in which case you must supply an index file to the '-n' option >> of grompp. >> >> This is my grompp line: >> grompp_mpi -f md.mdp -c nacl_palm_md_224.gro -p topol_nc.top -o >> nacl_palm_md_224_na.tpr -n select.ndx >> >> group system is defined like this in .top file: >> >> [ system ] >> ; Name >> NaCl >> >> P.S. >> Feel free to ask me more information, I am quite new in gromacs and I am >> not sure if I am giving you all the information. >> >> > The [system] directive just gives a name for output coordinate files and > such. It is not equivalent to the "System" index group. > > When reporting errors with groups, index files, etc, you need to provide > the text of the .mdp file and, at minimum, a listing of the groups in the > index file, e.g. from gmxcheck. > > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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. > -- 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.