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.
; 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> 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 | (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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