The error has told you, you have repeat energy groups, where at least one (and in your case all) of the atoms are placed within two energy groups.
Solution, define your energy groups so that you don't have atoms in more than one. You currently have: energygrps = Protein Protein Should be something like energygrps = Protein SOL Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of ???? ????? Sent: Monday, 11 October 2010 4:13 AM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] output force Unfortunately I've got an error. This is .mdp file: title = title cpp = /lib/cpp integrator = md tinit = 0.0 dt = 0.002 nsteps = 25000 nstcomm = 1 comm_grps = System ld_seed = -1 niter = 40 nstxout = 10000 nstvout = 0 nstfout = 0 nstlog = 500 nstenergy = 100 nstlist = 10 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb = 1.2 fourierspacing = 0.12 pme_order = 4 optimize_fft = yes pbc = xyz vdwtype = Cut-off rvdw = 1.2 tcoupl = V-rescale tc_grps = System tau_t = 0.1 ref_t = 300.0 annealing = single annealing_npoints = 3 annealing_time = 0 5 50 annealing_temp = 5 300 300 pcoupl = berendsen pcoupltype = isotropic compressibility = 4.5e-5 tau_p = 10.0 ref_p = 1.0 gen_vel = yes gen_temp = 5.0 gen_seed = -1 constraints = all-bonds constraint_algorithm = Lincs lincs_order = 4 disre = simple disre_weighting = conservative disre_mixed = no nstdisreout = 50000 disre_tau = 0 pull = constraint pull_geometry = distance pull_dim = Y Y Y pull_constr_tol = 1e-6 pull_nstfout = 1 pull_nstxout = 1 pull_ngroups = 1 pull_group0 = a pull_group1 = b pull_init1 = 0.700 pull_start = no pull_k1 = 1000 lincs_iter = 2 energygrps = Protein Protein I just replace in .mdp file line energygrps = System and the error is: Fatal error: Atom 1 in multiple Energy Mon. groups (1 and 2) What should I do to avoid this? 10 октября 2010 г. 20:01 пользователь Петр Попов <magistrpet...@gmail.com> написал: Thank you very much! 10 октября 2010 г. 19:58 пользователь Justin A. Lemkul <jalem...@vt.edu> написал: Петр Попов wrote: So if I want to get protein-solvent component I should add in .mdp: energygrps = Protein SOL ? Yes, and set nstlist = 1. -Justin 10 октября 2010 г. 16:41 пользователь Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>> написал: Петр Попов wrote: Thank you for response! One more question: How can I get file with energy groups? Should I use grompp with a -e ener.edr option? In this case, how to build ener.edr file? The "energrygrps" keyword is an .mdp option, so generate a new .tpr file with the desired groups and use the -rerun feature of mdrun on the trajectory that has already been produced. -Justin 9 октября 2010 г. 14:50 пользователь Mark Abraham <mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au> <mailto:mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>>> написал: You can get that with cunning use of energy groups and mdrun -rerun, but not mid-simulation. Mark ----- Original Message ----- From: Петр Попов <magistrpet...@gmail.com <mailto:magistrpet...@gmail.com> <mailto:magistrpet...@gmail.com <mailto:magistrpet...@gmail.com>>> Date: Saturday, October 9, 2010 21:41 Subject: [gmx-users] output force To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> > Hello dear gmx-users! > > When calculated forces in gromacs to produce pmf, we have the net force in output. For example: > ... > # > # Giving Russians Opium May Alter Current Situation > # > @ title "Pull force" > @ xaxis label "Time (ps)" > @ yaxis label "Force (kJ/mol/nm)" > @TYPE xy > 0.000000 1017490.761270 > 0.002000 -253098.034916 > 0.004000 -43856.400160 > 0.006000 48980.619113 > 0.008000 52103.053067 > 0.010000 33788.090031 > 0.012000 19096.388350 > 0.014000 14094.738810 > 0.016000 14027.621966 > 0.018000 15162.993741 > 0.020000 14136.978177 > ... etc. > > What sould I do to get the net force of protein-solvent interactions or protein-protein interactions or solvent-solvent interactions instead and get output .xvg file in the form like this: > > time Force(type1) Force(type2) Force(type3) > > t1 f1 f1 f1 > t2 f2 f2 f2 > t3 f3 f3 f3 > ... ... ... ... > etc. > > Thank you for attention and I hope you will help me! > -- > gmx-users mailing list gmx-users@gromacs.org <mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org <mailto: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 <mailto:gmx-users-requ...@gromacs.org> <mailto:gmx-users-requ...@gromacs.org <mailto:gmx-users-requ...@gromacs.org>>. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org <mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org <mailto: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 <mailto:gmx-users-requ...@gromacs.org> <mailto:gmx-users-requ...@gromacs.org <mailto:gmx-users-requ...@gromacs.org>>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org <mailto: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 <mailto:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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
-- 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
