Another way to try to understand what is going on wrong is to cut away
the residue 1 (atom 1)
and see what happens: in this case you will understand if the "guilty"
is the residue 1 (as LINCS seems, at least, to suggest) or anything else
in the protein.
Cheers
Luca
Dear Luca, dear all,
thank you for your hints. I made some trials with my systems and these are
my answers to your questions:
- my system is a protein (with or w/o ligand) in solvent (water SPC).
Following your suggestions, I tried to perform an EM on the protein w/o
ligand after the editconf step (i.e. I created the topology with pdb2gmx,
created a cubic box with editconf, then I used grompp+mdrun to perform EM).
I received the same error: the minimization starts, performs 37 steps, then
stops with the "stepsize too small...." communication. The energy in this
case is -3.06e+4 (one order of magnitude higher than the solvated system)
but still negative, and the maximum force is still "inf on atom 1". So
minimizing in vacuo does not help to solve the problem. This atom 1 is the
Nter of the protein, it is belonging to a Ser and I did not charge it
explicitly with pdb2gmx (i.e. I did not use the flag -ter) but it is bound
to 3 H in the .gro file.
- If I look at the protein with VMD or other visualizing tools, it seems to
me that no major problems are present on the structure. In particular, atom
1 is not "broken" or something similar, I can't see no "aberrations". I
don't know how to check if something goes wrong apart from visualization, do
you know some tools that could automatically check the file? To the best of
my knowledge, gmxcheck performs checks only on trajectories, or can I use it
also on single structures?
- I also tried to continue anyway after the minimization step with the PR MD
in NVT, but it did not start because of a lot of LINCS error. It suggests me
that some distortions are present in my structure, but if I cannot minimize
it, how to relieve this problem?
I copy&paste below the .log file for this new minimization in vacuo. The
parameters I used are the same for the minimization in solvent.
Any help will be appreciated.
Thank you very much and best regards
Input Parameters:
integrator = steep
nsteps = 50000
init_step = 0
ns_type = Grid
nstlist = 5
ndelta = 2
nstcomm = 1
comm_mode = Linear
nstlog = 100
nstxout = 100
nstvout = 100
nstfout = 0
nstenergy = 100
nstxtcout = 0
init_t = 0
delta_t = 0.001
xtcprec = 1000
nkx = 70
nky = 70
nkz = 70
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = No
epc = No
epctype = Isotropic
tau_p = 1
ref_p (3x3):
ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress (3x3):
compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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 = 1
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1.2
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 = no
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 = 0.1
em_tol = 1000
niter = 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake_tol = 0.0001
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: 6039
ref_t: 0
tau_t: 0
anneal: No
ann_npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp_flags[ 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 0.320163 nm for Ewald
Cut-off's: NS: 1 Coulomb: 1 LJ: 1.2
System total charge: -3.000
Generated table with 4400 data points for Ewald.
Tabscale = 2000 points/nm
Generated table with 4400 data points for LJ6.
Tabscale = 2000 points/nm
Generated table with 4400 data points for LJ12.
Tabscale = 2000 points/nm
Generated table with 4400 data points for 1-4 COUL.
Tabscale = 2000 points/nm
Generated table with 4400 data points for 1-4 LJ6.
Tabscale = 2000 points/nm
Generated table with 4400 data points for 1-4 LJ12.
Tabscale = 2000 points/nm
Configuring nonbonded kernels...
Testing x86_64 SSE2 support... present.
Removing pbc first time
Initiating Steepest Descents
Max number of connections per atom is 27
Total number of connections is 27956
Max number of graph edges per atom is 4
Total number of graph edges is 4086
Started Steepest Descents on node 0 Mon May 24 12:03:01 2010
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
Grid: 7 x 7 x 7 cells
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
2.40716e+03 1.23569e+03 6.85831e+02 8.70819e+01 2.11992e-314
Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip.
2.11992e-314 -2.19860e+03 -1.52663e+02 -6.70307e+03 -2.59368e+04
Potential Pressure (bar)
-3.05754e+04 nan
Step Time Lambda
1 1.00000 0.00000
Step Time Lambda
2 2.00000 0.00000
Step Time Lambda
3 3.00000 0.00000
Step Time Lambda
4 4.00000 0.00000
Step Time Lambda
5 5.00000 0.00000
Step Time Lambda
6 6.00000 0.00000
Step Time Lambda
7 7.00000 0.00000
Step Time Lambda
8 8.00000 0.00000
Step Time Lambda
9 9.00000 0.00000
Step Time Lambda
10 10.00000 0.00000
..........(same thing until)
Step Time Lambda
37 37.00000 0.00000
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax< 1000
Steepest Descents converged to machine precision in 38 steps,
but did not reach the requested Fmax< 1000.
Potential Energy = -3.05753603909389e+04
Maximum force = inf on atom 1
Norm of force = inf
Anna
Message: 2
Date: Fri, 21 May 2010 14:44:04 +0200
From: Luca Mollica<luca.moll...@ibs.fr>
Subject: Re: [gmx-users] stepsize too small ... but potential energy
negative!
To: Discussion list for GROMACS users<gmx-users@gromacs.org>
Message-ID:<4bf68014.1060...@ibs.fr>
Content-Type: text/plain; charset="iso-8859-1"
Dear Anna,
are you talking about a system "in vacuo" or in solvent ?
If you have placed the protein in water w/o minimizing it before
solvation, probabily an "in vacuo" minimization could be useful for your
system before moving into the solvated case. Moreover, are you sure that
the protein does not have "broken" residue or something like that ?
Sometimes, the completion of topology creation step goes fine but
something wrong (on the gromacs side, apart from visualization) with
sidechains or portion of the proteins that are generated by other
softwares/servers.
I do not think it's a ligand problem, BTW.
Cheers
Luca
Message: 3
Date: Fri, 21 May 2010 14:46:28 +0200
From: Luca Mollica<luca.moll...@ibs.fr>
Subject: Re: [gmx-users] stepsize too small ... but potential energy
negative!
To: gmx-users@gromacs.org
Message-ID:<4bf680a4.3060...@ibs.fr>
Content-Type: text/plain; charset="iso-8859-1"
Moreover,
the problem is not the potential energy, but the force that must converge.
The "inf" there about force and about atom 1 tells me that the computed
force has problems, indeed.
Which is atom 1 ? Is the protein Nter neutral or charged ? Or is atom 1
an atom from the ligand ?
Cheers
L
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