[gmx-users] PBC removing why?
David van der Spoel
spoel at xray.bmc.uu.se
Tue Aug 16 09:11:46 CEST 2005
On Mon, 2005-08-15 at 17:29 -0400, JAVIER SACRISTAN wrote:
> Hi Gromacs people,
>
>
> Then with genconf -f trajout.gro -nbox 3 3 3 -dist 1 -rot -o peo27.gro I have
> built a cell with 27 chains.
Here may be the problem. If your molecule is not in one piece you will
have
|
AAAAA|BBBBB
|
Meaning a serious mismatch between top and coords.
If you have a trajout.gro that is incorrect you may want to try trjconv
-pbc whole
> I don t understand what is going on? I have already checked Gromacs Users
> Mailing list archives, and I have found one mail about PBC errors, but the
> answer ( setenv GMXFULLPBC 1) was recommended for infinite systems /or rings.
> In my case it is a linear polymer.
>
This is handled now using
pbc = full
in 3.2.1 you can not combine this with constraints.
>
>
>
>
> I have included the log file.
>
> Any help would be really appreciated.
>
>
>
> Javier
>
>
>
>
>
> Input Parameters:
> integrator = md
> nsteps = 500000
> init_step = 0
> ns_type = Grid
> nstlist = 5
> ndelta = 2
> bDomDecomp = FALSE
> decomp_dir = 0
> nstcomm = 1
> nstcheckpoint = 1000
> nstlog = 500
> nstxout = 1000
> nstvout = 1000
> nstfout = 1000
> nstenergy = 500
> nstxtcout = 50
> init_t = 0
> delta_t = 0.002
> xtcprec = 1000
> nkx = 117
> nky = 117
> nkz = 117
> pme_order = 4
> ewald_rtol = 1e-05
> ewald_geometry = 0
> epsilon_surface = 0
> optimize_fft = FALSE
> ePBC = xyz
> bUncStart = FALSE
> bShakeSOR = FALSE
> etc = Berendsen
> epc = Berendsen
> epctype = Isotropic
> tau_p = 0.5
> ref_p (3x3):
> ref_p[ 0]={ 1.00000e+02, 0.00000e+00, 0.00000e+00}
> ref_p[ 1]={ 0.00000e+00, 1.00000e+02, 0.00000e+00}
> ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+02}
> compress (3x3):
> compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}
> compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}
> compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}
> andersen_seed = 815131
> rlist = 0.9
> coulombtype = Ewald
> rcoulomb_switch = 0
> rcoulomb = 0.9
> vdwtype = Cut-off
> rvdw_switch = 0
> rvdw = 0.9
> epsilon_r = 1
> tabext = 1
> gb_algorithm = Still
> nstgbradii = 1
> rgbradii = 2
> gb_saltconc = 0
> implicit_solvent = No
> DispCorr = EnerPres
> fudgeQQ = 1
> free_energy = no
> init_lambda = 0
> sc_alpha = 0
> sc_sigma = 0.3
> delta_lambda = 0
> disre_weighting = Conservative
> disre_mixed = FALSE
> dr_fc = 1000
> dr_tau = 0
> nstdisreout = 100
> orires_fc = 0
> orires_tau = 0
> nstorireout = 100
> dihre-fc = 1000
> dihre-tau = 0
> nstdihreout = 100
> em_stepsize = 0.01
> em_tol = 10000
> niter = 20
> fc_stepsize = 0
> nstcgsteep = 1000
> nbfgscorr = 10
> ConstAlg = Lincs
> shake_tol = 1e-04
> lincs_order = 4
> lincs_warnangle = 30
> lincs_iter = 1
> bd_temp = 300
> bd_fric = 0
> ld_seed = 1993
> cos_accel = 0
> userint1 = 0
> userint2 = 0
> userint3 = 0
> userint4 = 0
> userreal1 = 0
> userreal2 = 0
> userreal3 = 0
> userreal4 = 0
> grpopts:
> nrdf: 7449
> ref_t: 450
> tau_t: 0.1
> anneal: No
> ann_npoints: 0
> acc: 0 0 0
> nfreeze: N N N
> energygrp_excl[ 0]: 0
> efield-x:
> n = 0
> efield-xt:
> n = 0
> efield-y:
> n = 0
> efield-yt:
> n = 0
> efield-z:
> n = 0
> efield-zt:
> n = 0
> CPU= 0, lastcg= 404, targetcg= 202, myshift= 0
> nsb->shift = 1, nsb->bshift= 0
> Neighbor Search Blocks
> nsb->nodeid: 0
> nsb->nnodes: 1
> nsb->cgtotal: 405
> nsb->natoms: 2484
> nsb->shift: 1
> nsb->bshift: 0
> Nodeid index homenr cgload workload
> 0 0 2484 405 405
>
> Max number of graph edges per atom is 4
> Table routines are used for coulomb: TRUE
> Table routines are used for vdw: FALSE
> Using a Gaussian width (1/beta) of 0.288146 nm for Ewald
> Cut-off's: NS: 0.9 Coulomb: 0.9 LJ: 0.9
> Generated table with 500 data points for COUL.
> Tabscale = 500 points/nm
> Generated table with 500 data points for LJ6.
> Tabscale = 500 points/nm
> Generated table with 500 data points for LJ12.
> Tabscale = 500 points/nm
> Generated table with 950 data points for Ewald.
> Tabscale = 500 points/nm
> Generated table with 950 data points for LJ6.
> Tabscale = 500 points/nm
> Generated table with 950 data points for LJ12.
> Tabscale = 500 points/nm
> Going to determine what solvent types we have.
> There are 27 molecules, 405 charge groups and 2484 atoms
> There are 0 optimized solvent molecules on node 0
> There are 0 optimized water molecules on node 0
> Center of mass motion removal mode is Linear
> We have the following groups for center of mass motion removal:
> 0: rest, initial mass: 36495.8
> There are: 2484 Atom
> Removing pbc first time
> Done rmpbc
> Started mdrun on node 0 Mon Aug 15 14:50:12 2005
> Initial temperature: 449.96 K
> Step Time Lambda
> 0 0.00000 0.00000
>
> Grid: 30 x 30 x 30 cells
> There are 2484 atoms in your xtc output selection
>
> ++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
> H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
> Molecular dynamics with coupling to an external bath
> J. Chem. Phys. 81 (1984) pp. 3684-3690
> -------- -------- --- Thank You --- -------- --------
>
> Large VCM(group rest): -0.56846, -13.47183, -6.20070, ekin-cm:
> 4.01932e+06
> Long Range LJ corr. to Epot: -37.0893, Pres: -0.488348, Vir: 222.536
> Energies (kJ/mol)
> G96Bond G96Angle Proper Dih. LJ-14 Coulomb-14
> 3.58014e+03 5.23920e+03 4.07175e+03 -1.37463e+03 9.63356e+03
> LJ (SR) Disper. corr. Coulomb (SR) Coulomb (LR) Potential
> 8.36634e+12 -3.70893e+01 -1.95173e+02 -3.89469e+03 8.36634e+12
> Kinetic En. Total Energy Temperature Pressure (bar)
> 5.95690e+23 5.95690e+23 1.92360e+22 2.61444e+21
>
>
> Step 1 Warning: pressure scaling more than 1%, mu: 1.56867e+14 1.56867e+14
> 1.56867e+14
> Large VCM(group rest): -4140635995634663424.00000, 16562543982538653696.00000,
> -8281271991269326848.00000, ekin-cm: inf
> Grid: -2147483648 x -2147483648 x -2147483648 cells
> Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 218]
>
>
>
>
>
>
>
>
>
> Javier Sacristan Bermejo
> 115 Fenske Lab.
> Computer Polymer Simulations
> _______________________________________________
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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