[gmx-users] stepsize too small ... but potential energy negative!
Luca Mollica
luca.mollica at ibs.fr
Mon May 24 13:57:19 CEST 2010
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.mollica at ibs.fr>
> Subject: Re: [gmx-users] stepsize too small ... but potential energy
> negative!
> To: Discussion list for GROMACS users<gmx-users at gromacs.org>
> Message-ID:<4BF68014.1060706 at 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.mollica at ibs.fr>
> Subject: Re: [gmx-users] stepsize too small ... but potential energy
> negative!
> To: gmx-users at gromacs.org
> Message-ID:<4BF680A4.3060702 at 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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