[gmx-users] Not able to continue with Equilibration
francesca vitalini
francesca.vitalini11 at gmail.com
Thu Mar 29 17:00:36 CEST 2012
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>:
> 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
> --
> gmx-users mailing list gmx-users at gromacs.org
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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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