Dear all
i am trying to simulate a zinc-finger peptide using explicit solvent and g43a1
forcefield and backbone constraints . I have managed to simulate using
coulomb cut off for electrostatics. But i would also like to simulate using
PME. when i run the simulation at step 0 it gives constraint failure and
stops. i am at a loss.
I am attaching the mdp file and the log file
I would very much appreciate any help
have a nice weekend all
alpay
--
---------------------------------------------------
N. Alpay Temiz |
Department of Computational Biology & |
Department of Molecular Genetics and Biochemistry |
School of Medicine, University of Pittsburgh |
e-mail:[EMAIL PROTECTED] |
---------------------------------------------------
Log file opened: nodeid 0, nnodes = 1, host = structure, process = 7523
:-) G R O M A C S (-:
GROningen Mixture of Alchemy and Childrens' Stories
:-) VERSION 3.2.1 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2004, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) mdrun (-:
++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
-------- -------- --- Thank You --- -------- --------
++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
-------- -------- --- Thank You --- -------- --------
There are 0 atoms for free energy perturbation
Input Parameters:
integrator = md
nsteps = 5000000
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
bDomDecomp = FALSE
decomp_dir = 0
nstcomm = 1
nstcheckpoint = 1000
nstlog = 100
nstxout = 500
nstvout = 1000
nstfout = 0
nstenergy = 100
nstxtcout = 0
init_t = 0
delta_t = 0.001
xtcprec = 1000
nkx = 39
nky = 33
nkz = 39
pme_order = 6
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = xyz
bUncStart = FALSE
bShakeSOR = FALSE
etc = Berendsen
epc = Berendsen
epctype = Isotropic
tau_p = 0.5
ref_p (3x3):
ref_p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}
ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
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 = 1
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1
epsilon_r = 1
tabext = 1
gb_algorithm = Still
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
implicit_solvent = No
DispCorr = No
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 = 10
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: 650.934 29061.1 5.99939
ref_t: 300 300 300
tau_t: 0.1 0.1 0.1
anneal: No No No
ann_npoints: 0 0 0
acc: 0 0 0
nfreeze: N N N
energygrp_excl[ 0]: 0 0 0
energygrp_excl[ 1]: 0 0 0
energygrp_excl[ 2]: 0 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= 4975, targetcg= 2488, myshift= 0
nsb->shift = 1, nsb->bshift= 0
Neighbor Search Blocks
nsb->nodeid: 0
nsb->nnodes: 1
nsb->cgtotal: 4976
nsb->natoms: 14862
nsb->shift: 1
nsb->bshift: 0
Nodeid index homenr cgload workload
0 0 14862 4976 4976
Max number of graph edges per atom is 10
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
Cut-off's: NS: 1 Coulomb: 1 LJ: 1
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 1000 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1000 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 1000 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 4847 molecules, 4976 charge groups and 14862 atoms
There are 0 optimized solvent molecules on node 0
There are 4844 optimized water molecules on node 0
Will do PME sum in reciprocal space.
++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------
Using the FFTW library (Fastest Fourier Transform in the West)
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest, initial mass: 90884
There are: 14862 Atom
Removing pbc first time
Done rmpbc
Constraining the starting coordinates (step -2)
++++++++ 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 --- -------- --------
++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------
++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------
Initializing LINear Constraint Solver
number of constraints is 333
average number of constraints coupled to one constraint is 2.9
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.242540 55 56 0.025668
After LINCS 0.000341 318 326 0.000061
Going to use C-settle (4844 waters)
wo = 0.888096, wh =0.0559521, wohh = 18.0154, rc = 0.081665, ra = 0.00645837
rb = 0.051255, rc2 = 0.16333, rone = 1, dHH = 0.16333, dOH = 0.1
Constraining the coordinates at t0-dt (step -1)
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.038861 1 3 0.008525
After LINCS 0.000072 18 20 0.000015
Started mdrun on node 0 Fri Feb 24 20:47:13 2006
Initial temperature: 300.362 K
Step Time Lambda
0 0.00000 0.00000
Grid: 11 x 9 x 10 cells
Testing x86 processor CPUID...
CPU manufactured by Intel.
Testing x86 SSE capabilities...
CPU and OS support SSE.
Using Gromacs SSE single precision assembly innerloops.
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS inf 221 222 nan
After LINCS inf 104 105 nan
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max inf (between atoms 104 and 105) rms nan
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
104 105 91.8 0.1250 2093560579850265042993304043520.0000 0.1250
104 106 93.6 0.1250 1274146098171475800048667721728.0000 0.1250
134 135 91.2 0.1340 5534894030495869936863281152.0000 0.1340
134 138 94.1 0.1340 1413767884292467560372240384.0000 0.1340
135 136 90.0 0.1000 36211434633268531419989147648.0000 0.1000
135 137 90.5 0.1000 2770218450560423808745865216.0000 0.1000
138 139 90.1 0.1000 13633332910242591965114793984.0000 0.1000
138 140 92.6 0.1000 616323777556319235364356096.0000 0.1000
Constraint error in algorithm Lincs at step 0
t = 0.000 ps: Water molecule starting at atom 14858 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates
Energies (kJ/mol)
G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
5.75436e+02 1.19884e+02 7.23068e+00 2.65933e+02 2.25802e+03
LJ (SR) Coulomb (SR) Coulomb (LR) Position Rest. Potential
6.11002e+04 -2.18517e+05 nan 2.75587e-02 nan
Kinetic En. Total Energy Temperature Pressure (bar)
nan nan nan nan
;
; User spoel (236)
; Wed Nov 3 17:12:44 1993
; Input file
;
title = Yo
cpp = /lib/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.001 ; ps !
nsteps = 5000000 ; total 10 ps.
nstcomm = 1
nstxout = 500
nstvout = 1000
nstfout = 0
nstlog = 100
nstenergy = 100
nstlist = 10
ns_type = grid
coulombtype = pme
pme_order = 6
fourierspacing = 0.15
optimize_fft = yes
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc-grps = Protein SOL CL-
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300
; Energy monitoring
energygrps = Protein SOL CL-
; Pressure coupling is on
Pcoupl = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
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