Hi,
Thanks for your answer,
my pull_pbcatoms look like
pull_pbcatom0 belongs to the surface
pull_pbcatom2 belongs to the peptide
I will be happy if you could be more clear about
In principle pull_pbcatom0 can be any atom, it should not change a
predefined pulling rate
thanks
A.
Here is the log file
Input Parameters:
integrator = md
nsteps = 1000000
init_step = 0
ns_type = Grid
nstlist = 40
ndelta = 2
nstcomm = 1
comm_mode = Linear
nstlog = 5000
nstxout = 5000
nstvout = 5000
nstfout = 5000
nstenergy = 5000
nstxtcout = 2000
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 70
nky = 39
nkz = 49
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols = TRUE
bContinuation = FALSE
bShakeSOR = FALSE
etc = Berendsen
epc = Berendsen
epctype = Semiisotropic
tau_p = 1
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]={ 2.50000e-08, 0.00000e+00, 0.00000e+00}
compress[ 1]={ 0.00000e+00, 2.50000e-08, 0.00000e+00}
compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.00000e+00
posres_com[1]= 0.00000e+00
posres_com[2]= 0.00000e+00
posres_comB (3):
posres_comB[0]= 0.00000e+00
posres_comB[1]= 0.00000e+00
posres_comB[2]= 0.00000e+00
andersen_seed = 815131
rlist = 0.8
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 0.8
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 0.8
epsilon_r = 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = No
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
nwall = 0
wall_type = 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = umbrella
pull_geometry = position
pull_dim (3):
pull_dim[0]=1
pull_dim[1]=1
pull_dim[2]=0
pull_r1 = 1
pull_r0 = 1.5
pull_constr_tol = 1e-06
pull_nstxout = 100
pull_nstfout = 100
pull_ngrp = 1
pull_group 0:
atom (12558):
atom[0,...,12557] = {0,...,12557}
weight: not available
pbcatom = 6278
vec (3):
vec[0]= 0.00000e+00
vec[1]= 0.00000e+00
vec[2]= 0.00000e+00
init (3):
init[0]= 0.00000e+00
init[1]= 0.00000e+00
init[2]= 0.00000e+00
rate = 0
k = 0
kB = 0
pull_group 1:
atom (8):
atom[0,...,7] = {12665,...,12672}
weight: not available
pbcatom = 12668
vec (3):
vec[0]= 1.00000e+00
vec[1]= 0.00000e+00
vec[2]= 0.00000e+00
init (3):
init[0]=-5.39178e-01
init[1]= 1.09576e+00
init[2]= 0.00000e+00
rate = 0.01
k = 100
kB = 100
disre = No
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
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_fric = 0
ld_seed = 1993
cos_accel = 0
deform (3x3):
deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 36476.3 321.985 27568.7
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_flags[ 0]: 0 0 0
energygrp_flags[ 1]: 0 0 0
energygrp_flags[ 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
bQMMM = FALSE
QMconstraints = 0
QMMMscheme = 0
scalefactor = 1
qm_opts:
ngQM = 0
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Will do PME sum in reciprocal space.
++++ PLEASE READ AND 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 a Gaussian width (1/beta) of 0.25613 nm for Ewald
Cut-off's: NS: 0.8 Coulomb: 0.8 LJ: 0.8
System total charge: -0.000
Generated table with 900 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 900 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 900 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 900 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 900 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Enabling SPC water optimization for 4595 molecules.
Configuring nonbonded kernels...
Testing x86_64 SSE support... present.
Will apply umbrella COM pulling in geometry 'position'
between a reference group and 1 group
Pull group 0: 12558 atoms, mass 137674.546
Pull group 1: 8 atoms, mass 113.117
Initializing LINear Constraint Solver
++++ PLEASE READ AND 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 --- -------- --------
The number of constraints is 1219
++++ PLEASE READ AND 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 --- -------- --------
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: DIAM
++++ PLEASE READ AND 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 --- -------- --------
There are: 26458 Atoms
Constraining the starting coordinates (step 0)
Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 1.09e-06
Initial temperature: 300.134 K
Started mdrun on node 0 Thu May 27 12:03:34 2010
Step Time Lambda
0 0.00000 0.00000
Grid: 17 x 9 x 11 cells
Energies (kJ/mol)
Bond G96Bond Angle G96Angle Proper Dih.
4.90240e+04 1.53403e+02 9.28348e+04 2.23220e+02 1.41487e+02
Ryckaert-Bell. Improper Dih. LJ-14 Coulomb-14 LJ (SR)
4.83454e+05 5.14344e+01 -1.62957e+01 1.71089e+03 -2.68920e+04
Coulomb (SR) Coul. recip. COM Pull En. Potential Kinetic En.
-1.88099e+05 -3.41786e+04 2.58240e-12 3.78407e+05 8.04666e+04
Total Energy Temperature Pressure (bar) Cons. rmsd ()
4.58874e+05 3.00708e+02 2.08080e+03 1.09884e-06
[email protected] wrote:
Read about the .mdp options pull_pbcatom0 and pull_pbcatom1
-- original message --
Hi everyone,
I have a pulling code running on single machine with Gromacs 4.0.7
The systems composes of a surface, a protein and water
I pull the protein from the terminal group on the surface laterally.
With Gromacs 3.3.3 (on single processors ) the setup works perfectly and
generates correct results for pulling positions compared to g_traj...
To be able use periodic molecules (for the surface), I switched to
gromacs 4.0.7 and I use the "position" option to reproduce the previous
v3 results.
The problem is that the pullf.xvg gives negative forces...
Normally, the pulling force should reach a pseudo-constant level but in
my case it just keep going toward minus infinity (unless I cease the run)
Also when I checked position of the pulled group I see that the tangent
of the displacement-time curve (which is th pulling rate) is also
increasing afte.
This is bit irrational since the pulling rate is set constant at the
first place...
For instance, with a pulling rate of 10nm/ns in 1ns you should have
displacement of roughly 10nm.
Untill 0.4 ns everything looks ok but then (when the peptide moves to
the next periodic box) velocity increases and I have a displacement of
more 150nm within 1ns...
Also, I must say that in the trajectory the increasing velocity of the
pulled can be seen clearly with naked-eye.
Here is my mdp file;
integrator = md
nsteps = 1000000
dt = 0.002
nstlist = 40
nstxout = 5000
nstvout = 5000
nstfout = 5000
nstxtcout = 2000
nstlog = 5000
nstenergy = 5000
constraints = hbonds
ns_type = grid
coulombtype = pme
pme_order = 4
fourierspacing = 0.12
rlist = 0.8
rvdw = 0.8
rcoulomb = 0.8
energygrps = DIAM Protein SO
tcoupl = berendsen
tc_grps = DIAM Protein SOL
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300
gen_vel = no
Pcoupl = berendsen
Pcoupltype = semiisotropic
compressibility = 2.5E-8 4.5E-5
tau_p = 1.0 1.0
ref_p = 1.0 1.0
comm_mode = angular
comm_grps = DIAM
periodic_molecules = yes
pbc = xyz
;PULLING
pull = umbrella
pull_start = yes
pull_geometry = position
pull_nstxout = 100
pull_nstfout = 100
pull_ngroups = 1
pull_group0 = DIAM
pull_group1 = AA1
pull_vec1 = 1.0 0.0 0.0
pull_init1 = 0.0 0.0 0.0
pull_rate1 = 0.01
pull_k1 = 100
--
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