[gmx-users] Not able to continue with Equilibration
chris.neale at utoronto.ca
chris.neale at utoronto.ca
Thu Mar 29 17:19:04 CEST 2012
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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