[gmx-users] Not able to continue with Equilibration
francesca vitalini
francesca.vitalini11 at gmail.com
Thu Mar 29 23:39:36 CEST 2012
Thank you Justin for your answer. I'm trying to add the position
restraints to my protein, but I have a problem. My topology is made of
a chain repeated twice and if I want to build the position restraints
through genrestr from a gro file, the numeration of the atoms would
put the 2 chains sequentially one after the other, but then the index
would be out of bounds; if I try to generate the topology from x2top
it has been taking more than 6 hours and hasn't finish yet. If instead
I try to use the posre.itp built from pdb2gmx I still have the LINCS
warnings, even after changing rlist, rcoulomb and rvdw to 1. Any ideas
on a faster way to add my position restraints or how to solve the
LINCS error? Thank you very much.
Francesca
2012/3/29 Justin A. Lemkul <jalemkul at vt.edu>:
>
>
> francesca vitalini wrote:
>>
>> 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 naďve, 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?
>
>
> You should likely be restraining your protein, not the water. Bad initial
> geometry (sometimes stuff survives EM) can give your structure a nasty kick
> that causes things to spin out of control. Restraints on the protein
> mitigate these effects while the water relaxes.
>
> -Justin
>
>
>> 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
>>>
>>> -
>>>
>>>
>>> --
>>> gmx-users mailing list gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
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>>
>>
>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
> --
> 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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