And what if I have four helices in Protein and a,b,c,d group for each helix in index.file and I want to get a-c pmf?
10 октября 2010 г. 21:20 пользователь Justin A. Lemkul <jalem...@vt.edu>написал: > > > Justin A. Lemkul wrote: > >> >> >> Петр Попов wrote: >> >>> 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 >>> >> > If this .mdp file is to be used for a rerun, please recall the advice I > gave you earlier about the proper setting for nstlist. > > -Justin > > > 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? >>> >>> >> You cannot use multiple energygrps if those groups overlap in any way, as >> the error indicates. I thought you were setting "energygrps = Protein SOL"? >> If you're trying to get protein-only terms, then just set "energygrps = >> Protein" >> >> -Justin >> >> >>> >>> 10 октября 2010 г. 20:01 пользователь Петр Попов < >>> magistrpet...@gmail.com <mailto:magistrpet...@gmail.com>> написал: >>> >>> Thank you very much! >>> >>> 10 октября 2010 г. 19:58 пользователь Justin A. Lemkul >>> <jalem...@vt.edu <mailto: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> >>> <mailto: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>> >>> <mailto: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>> >>> <mailto: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>> >>> <mailto: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>> >>> <mailto: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>> >>> <mailto: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>> >>> <mailto: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>> >>> <mailto: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> <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> >>> <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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