[gmx-users] PBC removing why?
JAVIER SACRISTAN
jus29 at psu.edu
Mon Aug 15 23:29:01 CEST 2005
Hi Gromacs people,
I'm working to perform molecular dynamics simulations of 27 polymer chains in
PBC and I have
found some problems.
After preliminary minimization and equilibration of one chain under PBC and NPT
by means of trjconv I have extracted the coordinates for my polymer chain ( I
am interested in some specific conformation=specific frame on the trajectory
file).
Then with genconf -f trajout.gro -nbox 3 3 3 -dist 1 -rot -o peo27.gro I have
built a cell with 27 chains.
Finally with
grompp -f peo25.mdp -p peo25.top -c tpeo25.gro -o peo25.tpr I have generated
tpr file.
But unfortunately when I run the simulation I have got this message on the log
file:
Removing PBC first time.
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.
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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