If gromacs assumes the aminoacid residues as charge groups by default then I have many residues which have 12 atoms since I am using an all-atom force field-charmm27(counting H).
Is there a way to define charge groups? On Sat, Jul 17, 2010 at 7:41 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Sai Pooja wrote: > >> Thanks Justin. How about note 3? >> >> The largest charge group contains 12 atoms. >> Since atoms only see each other when the centers of geometry of the >> charge >> groups they belong to are within the cut-off distance, too large charge >> groups can lead to serious cut-off artifacts. >> For efficiency and accuracy, charge group should consist of a few atoms. >> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. >> >> This note reappears no matter what the parameter file has. Does this mean >> I need to make changes in my top file or define charge groups? >> >> > Yes, something is wrong with the topology. You have a charge group that is > likely unacceptably large. > > -Justin > > Pooja >> >> >> >> On Sat, Jul 17, 2010 at 7:25 AM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Sai Pooja wrote: >> >> Hi, >> >> This is the .mdp file that produces notes-3 and 4. However, the >> previous md file produces note-3. >> >> ; RUN CONTROL PARAMETERS >> integrator = md >> dt = 0.002 >> nsteps = 5000000 >> >> ; OUTPUT CONTROL OPTIONS >> nstxout = 0 ; No output, >> except for last frame (coordinates) >> nstvout = 0 ; No output, >> except for last frame (velocities) >> nstfout = 0 ; No output, >> except for last frame (forces) >> nstlog = 500000 ; Write every >> step to the log >> nstenergy = 500000 ; Write >> energies at every step >> xtc_grps = Protein >> nstxtcout = 500000 ; Do not >> write a compressed trajectory >> energygrps = Protein Non-Protein ; Write energy >> information separately for these groups >> >> ; NEIGHBORSEARCHING PARAMETERS >> nstlist = 5 >> ns-type = Grid >> pbc = xyz >> rlist = 2.0 >> >> ; OPTIONS FOR ELECTROSTATICS AND VDW >> coulombtype = Reaction-field-zero >> rcoulomb = 1.8 >> epsilon_rf = 0 >> vdw-type = Switch >> rvdw = 2.0 >> rvdw-switch = 1.6 >> >> >> Well, here's the problem. Read about proper usage of the switch >> function, especially the note about the size of rlist: >> >> http://manual.gromacs.org/current/online/mdp_opt.html#vdw >> >> -Justin >> >> ; Spacing for the PME/PPPM FFT >> fourierspacing = 0.12 >> ; FFT grid size, when a value is 0 fourierspacing will be used = >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> ; EWALD/PME/PPPM parameters = >> pme_order = 4 >> ewald_rtol = 1e-05 >> epsilon_surface = 0 >> optimize_fft = no >> ; Temperature coupling >> tcoupl = nose-hoover >> tc-grps = Protein Non-Protein >> tau_t = 0.2 0.2 >> ref_t = 300 300 >> >> ; Pressure coupling pcoupl = no >> >> ; OPTIONS FOR BONDS constraints = all-bonds >> constraint-algorithm = SHAKE >> shake_tol = 0.0001 >> >> Pooja >> >> >> >> On Fri, Jul 16, 2010 at 8:51 PM, Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> Sai Pooja wrote: >> >> Hi, >> >> I am trying to reproduce results from a paper which uses >> this >> cutoff. The work is on loop-folding and they use implicit >> solvent. I am using explicit solvent with charmm 27. >> Below is my >> mdp file. I am not sure if there is any advantage in using a >> large cut-off. >> >> >> >> Large cutoffs can cause artifacts. This .mdp file also does not >> match the error message you quoted before. If it is indeed >> accurate, then it looks like your .mdp file is being interpreted >> incorrectly (2.0-nm cutoffs instead of 1.8 nm). If there is a >> misinterpretation, file a bugzilla. If you've simply posted the >> wrong file, please post the correct file, if necessary. But I'd >> suggest you do some homework about the effects of long cutoffs, >> especially if they deviate from what the force field derivation >> requires. >> >> -Justin >> >> ; VARIOUS PREPROCESSING OPTIONS >> title = NVT simulation (constant number, >> pressure and temperature) >> cpp = /lib/cpp >> define =-DPOSRES >> >> ; RUN CONTROL PARAMETERS >> integrator = md >> dt = 0.002 >> nsteps = 100000 >> >> ; OUTPUT CONTROL OPTIONS >> nstxout = 10000 >> nstvout = 0 >> nstfout = 0 >> nstlog = 10000 >> nstenergy = 10000 >> nstxtcout = 0 >> xtc_precision = 0 >> xtc-grps = System >> energygrps = Protein Non-Protein >> >> ; NEIGHBORSEARCHING PARAMETERS >> nstlist = 5 >> ns-type = Grid >> pbc = xyz >> rlist = 1.8 >> >> ; OPTIONS FOR ELECTROSTATICS AND VDW >> coulombtype = PME >> fourierspacing = 0.12 >> rcoulomb = 1.8 >> epsilon_rf = 78 >> vdw-type = Cut-off >> rvdw = 1.8 >> >> ; FFT grid size, when a value is 0 fourierspacing will be >> used = >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> ; EWALD/PME/PPPM parameters = >> pme_order = 4 >> ewald_rtol = 1e-05 >> epsilon_surface = 0 >> optimize_fft = no >> >> ; Temperature coupling Tcoupl = Berendsen >> tc-grps = Protein Non-Protein >> tau_t = 0.2 0.2 >> ref_t = 300 300 >> >> ; Pressure coupling Pcoupl = Berendsen >> Pcoupltype = Isotropic >> tau_p = 1.0 >> compressibility = 4.5e-5 >> ref_p = 1.0 >> >> ; GENERATE VELOCITIES FOR STARTUP RUN >> gen_vel = no ; Assign velocities to >> particles by taking them randomly from a Maxwell >> distribution >> gen_temp = 300.0 ; Temperature to generate >> corresponding Maxwell distribution >> gen_seed = 9999 ; Seed for (semi) random >> number generation. >> >> >> ; OPTIONS constraints = all-bonds >> >> Pooja >> >> >> >> >> >> >> >> On Fri, Jul 16, 2010 at 8:22 PM, Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> wrote: >> >> >> >> Sai Pooja wrote: >> >> Hi, >> >> I am getting these notes when I run grompp: >> >> NOTE 3 [file Init/ffsb_init.top]: >> The largest charge group contains 12 atoms. >> Since atoms only see each other when the centers of >> geometry of >> the charge >> groups they belong to are within the cut-off >> distance, too >> large charge >> groups can lead to serious cut-off artifacts. >> For efficiency and accuracy, charge group should >> consist >> of a >> few atoms. >> For all-atom force fields use: CH3, CH2, CH, NH2, >> NH, >> OH, CO2, >> CO, etc. >> >> initialising group options... >> processing index file... >> Analysing residue names: >> There are: 3484 OTHER residues >> There are: 67 PROTEIN residues >> There are: 0 DNA residues >> There are: 0 RNA residues >> Analysing Protein... >> Analysing Other... >> Making dummy/rest group for Acceleration >> containing 11343 >> elements >> Making dummy/rest group for Freeze containing >> 11343 elements >> Making dummy/rest group for VCM containing 11343 >> elements >> Number of degrees of freedom in T-Coupling group >> Protein >> is 1777.76 >> Number of degrees of freedom in T-Coupling group >> non-Protein is >> 20898.23 >> Making dummy/rest group for User1 containing 11343 >> elements >> Making dummy/rest group for User2 containing 11343 >> elements >> Making dummy/rest group for XTC containing 10450 >> elements >> Making dummy/rest group for Or. Res. Fit >> containing 11343 >> elements >> Making dummy/rest group for QMMM containing 11343 >> elements >> T-Coupling has 2 element(s): Protein >> non-Protein >> Energy Mon. has 2 element(s): Protein >> non-Protein >> Acceleration has 1 element(s): rest >> Freeze has 1 element(s): rest >> User1 has 1 element(s): rest >> User2 has 1 element(s): rest >> VCM has 1 element(s): rest >> XTC has 2 element(s): Protein rest >> Or. Res. Fit has 1 element(s): rest >> QMMM has 1 element(s): rest >> Checking consistency between energy and charge >> groups... >> Largest charge group radii for Van der Waals: >> 0.288, 0.263 nm >> Largest charge group radii for Coulomb: >> 0.288, 0.263 nm >> >> NOTE 4 [file nvtp.mdp]: >> The sum of the two largest charge group radii >> (0.551009) is >> larger than >> rlist (2.000000) - rvdw (2.000000) >> >> Can someone tell me how to correct these? >> >> >> Note 3 is explained in detail in the error message. >> Beyond that, >> read about the group concept in the manual. >> >> I've never seen Note 4 before, but a 2-nm cutoff is a >> bit strange >> for a protein simulation. Any reason you're using >> such large >> cutoffs? You may also want to provide your whole .mdp >> file >> to see >> if anyone can spot the underlying issue. >> >> -Justin >> >> -- ======================================== >> >> 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> >> <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 >> >> >> <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/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/mailing_lists/users.php >> >> >> >> >> -- Quaerendo Invenietis-Seek and you shall discover. >> >> >> -- ======================================== >> >> 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/searchbefore >> 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/mailing_lists/users.php >> >> >> >> >> -- Quaerendo Invenietis-Seek and you shall discover. >> >> >> -- ======================================== >> >> 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/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/mailing_lists/users.php >> >> >> >> >> -- >> Quaerendo Invenietis-Seek and you shall discover. >> > > -- > ======================================== > > 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/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/mailing_lists/users.php > -- Quaerendo Invenietis-Seek and you shall discover.
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