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 >> > >
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