[gmx-users] Not able to continue with Equilibration

francesca vitalini francesca.vitalini11 at gmail.com
Thu Mar 29 17:30:30 CEST 2012


My minimization was done without any constraints. I'm starting using
constraints only in the nvt equilibration as I'm trying to equilibrate
my solvent, so, maybe here I'm being extremely naïve, but, shouldn't I
avoid fixing the water in the nvt, as equilibrating it is exactly the
reason I'm running the nvt equilibration? Or am I misunderstanding
something?
Thanks
Francesca



2012/3/29  <chris.neale at utoronto.ca>:
> I didn't follow this whole thread, but I sometimes need to turn off all
> constraints when doing minimization. In fact, for that reason I entirely
> stopped ever using restraints during energy minimization. In extreem cases,
> I have had success also by forcing the water to be flexible with a
> -DFLEXIBLE (or whatever is appropriate for your water model; check the .itp)
> statement in the .mdp file.
>
> Once EM is done, use rigid water and restraints and everything works out ok.
>
> Chris.
>
> -- original message --
>
> Hallo Felix,
> thank you for your answer. I tried the constraints = h-bonds but no
> change in the output. If I look at the step.pdb file that is produced
> after the running I have some strange outcome. For example some of my
> atoms are not recognized as part of my protein any more and my
> structure is destroied. Am I using some strange parameters for nvt
> without realizing it? I've started from the mdp file provided by the
> lysozyme tutorial non the Gromacs webpage.
> if anyone has any ideas it is more than welcome.
> Francesca
>
> integrator      = md            ; leap-frog integrator
> nsteps          = 10000         ; 2 * 10000 = 20 ps
> dt              = 0.002         ; 2 fs
> ; Output control
> nstxout         = 1             ; save coordinates every 0.2 ps
> nstvout         = 1             ; save velocities every 0.2 ps
> nstenergy       = 50            ; save energies every 0.2 ps
> nstlog          = 50            ; update log file every 0.2 ps
> ; Bond parameters
> unconstrained_start = no
> ;continuation   = no            ; first dynamics run
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = h-bonds       ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter      = 1             ; accuracy of LINCS
> lincs_order     = 4             ; also related to accuracy
> ; Neighborsearching
> ns_type         = grid          ; search neighboring grid cells
> nstlist         = 5             ; 10 fs
> rlist           = 3.0           ; short-range neighborlist cutoff (in nm)
> rcoulomb        = 3.0           ; short-range electrostatic cutoff (in nm)
> rvdw            = 3.0           ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype     = PME           ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order       = 4             ; cubic interpolation
> fourierspacing  = 0.16          ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl          = berendsen     ; modified Berendsen thermostat
> tc-grps         = Protein Non-Protein   ; two coupling groups - more
> accurate
> tau_t           = 0.1 0.1       ; time constant, in ps
> ref_t           = 300 300               ; reference temperature, one
> for each group, in K
> ; Pressure coupling is off
> pcoupl          = no            ; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc             = xyz           ; 3-D PBC
> ; Dispersion correction
> DispCorr        = EnerPres      ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel         = yes           ; assign velocities from Maxwell
> distribution
> gen_temp        = 300           ; temperature for Maxwell distribution
> gen_seed        = -1            ; generate a random seed
>
>
>
> 2012/3/29 Rausch, Felix <frausch at ipb-halle.de>:
>
> [Hide Quoted Text]
> Hello again,
>
> Well, I once had problems with simulations crashing randomly during
> production runs (sometimes after tens of nanoseconds) with the LINCS
> warnings you described. Switching LINCS from "all-bonds" to only "h-bonds"
> did the trick for me, although I never exactly figured out why.
> Maybe it's worth a try for you, too?
> Cheers,
> Felix
>
> -----Ursprüngliche Nachricht-----
> Von: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] Im
> Auftrag von francesca vitalini
> Gesendet: Donnerstag, 29. März 2012 15:15
> An: Discussion list for GROMACS users
> Betreff: Re: [gmx-users] Not able to continue with Equilibration
>
> Hi!
> I'm having a similar problem. I have a dimer solvated in a big box of water
> plus ions that I have managed to minimize correctly (see output of
> minimization at the end) but when I try to run NVT equilibration (see later)
> I get LINCS warnings(see below) refearred to atoms which are not in a
> cluster or in a strange position. I have added dihedral restraints on them
> but still the same type of error. I'm using GROMACS 3.3.1. I have tried to
> switch to a newer version of GROMACS but still the same error.
> Does anyone have any suggestions?
> Thanks
> Francesca
>
>
> MINIMIZATION OUTPUT
>
> Steepest Descents converged to Fmax < 1000 in 681 steps Potential Energy  =
> -1.9597512e+07
> Maximum force     =  2.4159846e+02 on atom 13087
> Norm of force     =  2.1520395e+04
>
>
> MINIMIZATION.MDP
>
> define         = -DEFLEXIBLE ; flexible water
> integrator      = steep         ; Algorithm (steep = steepest descent
> minimization)
> emtol           = 1000.0         ; Stop minimization when the maximum
> force < 1000.0 kJ/mol/nm
> emstep          = 0.001          ; Energy step size
> nsteps          = 50000         ; Maximum number of (minimization)
> steps to perform
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist         = 1             ; Frequency to update the neighbor
> list and long range forces
> ns_type         = grid          ; Method to determine neighbor list
> (simple, grid)
> rlist           = 1.0           ; Cut-off for making neighbor list
> (short range forces)
> coulombtype     = PME           ; Treatment of long range
> electrostatic interactions
> rcoulomb        = 1.0           ; Short-range electrostatic cut-off
> rvdw            = 1.0           ; Short-range Van der Waals cut-off
> pbc             = xyz           ; Periodic Boundary Conditions (yes/no)
>
>
> NVT.MDP
>
> define          = -DPOSRES      ; position restrain the protein
> ; Run parameters
> integrator      = md            ; leap-frog integrator
> nsteps          = 10000         ; 2 * 10000 = 20 ps
> dt              = 0.002         ; 2 fs
> ; Output control
> nstxout         = 50            ; save coordinates every 0.2 ps
> nstvout         = 50            ; save velocities every 0.2 ps
> nstenergy       = 50            ; save energies every 0.2 ps
> nstlog          = 50            ; update log file every 0.2 ps
> ; Bond parameters
> unconstrained_start = no
> ;continuation   = no            ; first dynamics run
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter      = 1             ; accuracy of LINCS
> lincs_order     = 4             ; also related to accuracy
> ; Neighborsearching
> ns_type         = grid          ; search neighboring grid cells
> nstlist         = 5             ; 10 fs
> rlist           = 3.0           ; short-range neighborlist cutoff (in nm)
> rcoulomb        = 3.0           ; short-range electrostatic cutoff (in nm)
> rvdw            = 3.0           ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype     = PME           ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order       = 4             ; cubic interpolation
> fourierspacing  = 0.16          ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl          = berendsen     ; modified Berendsen thermostat
> tc-grps         = Protein Non-Protein   ; two coupling groups - more
> accurate
> tau_t           = 0.1 0.1       ; time constant, in ps
> ref_t           = 300 300               ; reference temperature, one
> for each group, in K
> ; Pressure coupling is off
> pcoupl          = no            ; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc             = xyz           ; 3-D PBC
> ; Dispersion correction
> DispCorr        = EnerPres      ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel         = yes           ; assign velocities from Maxwell
> distribution
> gen_temp        = 300           ; temperature for Maxwell distribution
> gen_seed        = -1            ; generate a random seed
>
> ; Dihedral restraints
>
> dihre               =  simple ; Some dihedrals are restrained  for
> instance peptide bonds are set to trans conformation.
> dihre_fc            =  500
> dihre_tau           =  0.0
> nstdihreout         =  50
>
> NVT LINCS ERROR
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.002851 (between atoms 10721 and 10723) rms 0.000161 bonds that rotated
> more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>   672    673   33.7    0.1000   0.1000      0.1000
>  1081   1082   33.8    0.1000   0.1000      0.1000
>  1647   1648   34.4    0.1000   0.1000      0.1000
>  2819   2820   37.1    0.1000   0.1000      0.1000
>  2920   2921   39.6    0.1000   0.1000      0.1000
>  4090   4091   35.2    0.1000   0.1000      0.1000
>  4727   4728   37.2    0.1000   0.1000      0.1000
>  5160   5161   31.7    0.1000   0.1000      0.1000
>  6824   6825   33.3    0.1000   0.1000      0.1000
> ...
> step 0
> Step 1, time 0.002 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.017976 (between atoms 14692 and 14693) rms 0.000520 bonds that rotated
> more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>   672    673   67.8    0.1000   0.0999      0.1000
> ....
>
> Step 2, time 0.004 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.060681 (between atoms 6906 and 6907) rms 0.001874 bonds that rotated
> more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>   672    673   80.8    0.0999   0.0999      0.1000
>  1081   1082   90.0    0.1000   0.1008      0.1000
>  ...
>
> Step 3, time 0.006 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.104238 (between atoms 10603 and 10604) rms 0.003281 bonds that rotated
> more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>   672    673   67.1    0.0999   0.1000      0.1000
>  1081   1082   69.6    0.1008   0.1000      0.1000
> ...
>
> Step 4, time 0.008 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.569872 (between atoms 8709 and 8710) rms 0.013041 bonds that rotated
> more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>   672    673   40.3    0.1000   0.1000      0.1000
>  1081   1082   39.6    0.1000   0.1000      0.1000
>  1249   1250   37.6    0.1000   0.1000      0.1000
> ...
>
> Step 5, time 0.01 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 2.761976 (between atoms 8202 and 8204) rms 0.056483 bonds that rotated
> more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>  3320   3321   43.0    0.1090   0.1090      0.1090
>  3875   3876   32.0    0.1090   0.1090      0.1090
>  4013   4014   34.3    0.1090   0.1082      0.1090
>  4070   4071   42.1    0.1092   0.1092      0.1090
>  4072   4073   45.2    0.1090   0.1086      0.1090
>  4727   4729   34.2    0.1007   0.1002      0.1000
>  4961   4962   31.4    0.1091   0.1089      0.1090
>  4992   4993   46.0    0.1091   0.1089      0.1090
>  8159   8160   30.9    0.1251   0.1465      0.1230
>  ...
>
> Step 6, time 0.012 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 22.009092 (between atoms 8202 and 8204) rms 0.488487 bonds that rotated
> more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>  2920   2921   44.7    0.1000   0.1001      0.1000
>  3320   3321   36.6    0.1090   0.1087      0.1090
>  3592   3593   32.1    0.1090   0.1089      0.1090
>  ....
> Warning: 1-4 interaction between 8159 and 8168 at distance 1.580 which is
> larger than the 1-4 table size 1.000 nm These are ignored for the rest of
> the simulation This usually means your system is exploding, if not, you
> should increase table-extension in your mdp file
>
> Step 7, time 0.014 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 403.393890 (between atoms 8202 and 8204) rms 8.430617 bonds that rotated
> more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>   302    303   31.7    0.1003   0.1001      0.1000
>   672    673   66.4    0.1001   0.1001      0.1000
>  1050   1051   33.1    0.1003   0.1003      0.1000
>  1081   1082   46.7    0.1000   0.1000      0.1000
>  1225   1226   35.0    0.1003   0.1003      0.1000
>  ....
>
> Wrote pdb files with previous and current coordinates
>
> Step 8, time 0.016 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 7568.298828 (between atoms 8202 and 8204) rms 155.435715 bonds that
> rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>   205    206   31.6    0.1003   0.1002      0.1000
>   302    303   36.9    0.1001   0.1002      0.1000
>   672    673   76.0    0.1001   0.0997      0.1000
>  1050   1051   34.3    0.1003   0.1003      0.1000
>  1081   1082   63.0    0.1000   0.0999      0.1000
>  1225   1226   36.6    0.1003   0.1003      0.1000
>  1249   1250   38.7    0.1001   0.1001      0.1000
>  1647   1648   62.8    0.1000   0.0996      0.1000
>  1679   1680   42.5    0.1000   0.1000      0.1000
>  2214   2215   31.6    0.1002   0.1001      0.1000
>  2577   2578   31.1    0.1003   0.1002      0.1000
>  2819   2820   68.0    0.1000   0.0997      0.1000
>  2920   2921   71.5    0.1023   0.1000      0.1000
>  3468   3469   34.7    0.1092   0.1090      0.1090
>  3676   3677   34.7    0.1090   0.1090      0.1090
>  3714   3717   34.7    0.0998   0.0999      0.1000
>  3746   3747   70.8    0.1086   0.1069      0.1090
> ....
>
> Back Off! I just backed up step7.pdb to ./#step7.pdb.1# Wrote pdb files with
> previous and current coordinates
>
> Step 9, time 0.018 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 148599.687500 (between atoms 8202 and 8204) rms 3002.328125 bonds that
> rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length ....
>
> Back Off! I just backed up step8.pdb to ./#step8.pdb.1# Wrote pdb files with
> previous and current coordinates Segmentation fault
>
>
> 2012/3/29 Mark Abraham <Mark.Abraham at anu.edu.au>:
> On 29/03/2012 8:22 PM, Hendry wrote:
>
> Hi,
>
>
>
> I am using Gromacs 4.5.4. After successful minimization by SD, I
> continued with equilibration step but I got the below errors. I tried
> many times with different parameters but the problem still persists. I
> have given errors and md parameters of equilibration step below. I
> have also provided my minimization output at the end. Could you
> provide some suggestions what went wrong?.
>
>
> You are using PR-pressure coupling for equilibration, which is an
> unstable combination. You are coupling ions to their own thermostat,
> which is unstable. Do check out the GROMACS manual for discussion of
> how these algorithms work, and also the website for some practical
> observations.
>
> Mark
>
> -
>
>
> --
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-- 
Francesca Vitalini

PhD student at Computational Molecular Biology Group,
Department of Mathematics and Informatics, FU-Berlin
Arnimallee 6 14195 Berlin

vitalini at zedat.fu-berlin.de
francesca.vitalini at fu-berlin.de

+49 3083875776
+49 3083875412



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