[gmx-users] Lincs warning_set GMX_MAXCONSTRWARN to -1
Naveen BK
naveenbk4717 at gmail.com
Thu Apr 4 09:29:48 CEST 2019
Hi,
The minimization problem you can solve by increasing the water box size( I
guess) and in the NVT step edit mdp file, there change "constraints =
all-bonds" into constraints = h-bonds". This worked for me long before.
Check the link error where you will find atom numbers, and you can use
Avogadro, Chimera or any other tools which do geometrical optimization.
On Thu, Apr 4, 2019 at 12:12 PM Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> Hi,
>
> The largest force on an atom is reported by the minimization is enormous.
> Proceeding on with equilibration is unlikely to succeed. Look at the region
> around the atom whose number is reported and see what unphysical thing is
> happening there.
>
> Mark
>
> On Thu., 4 Apr. 2019, 08:31 Anjali Patel, <anjalipatel60316 at gmail.com>
> wrote:
>
> > Hello users,
> >
> > Yes i have gone through all lincs warning from the errors and also i have
> > refer user mailing list for this trouble. But i am not getting the
> answer.
> > i am doing MD simulation in which i have minimized system number of times
> > and my "em.mdp" file is blowed.
> >
> > ; LINES STARTING WITH ';' ARE COMMENTS
> > title = Minimization ; Title of run
> >
> > ; Parameters describing what to do, when to stop and what to save
> > integrator = steep ; Algorithm (steep = steepest
> > descent minimization)
> > emtol = 1000.0 ; Stop minimization when the maximum
> force
> > < 10.0 kJ/mol
> > emstep = 0.002 ; Energy step size
> > nsteps = 50000 ; Maximum number of
> (minimization)
> > steps to perform
> > nbfgscorr = 10
> > constraints = none
> > ; Parameters describing how to find the neighbors of each atom and how to
> > calculate the intee
> > ractions
> > nstlist = 1 ; Frequency to update the
> neighbor
> > list and long rann
> > ge forces
> > cutoff-scheme = Verlet
> > ewald_rtol = 1e-6
> > ns_type = grid ; Method to determine
> neighbor
> > list (simple, grii
> > d)
> > rlist = 1.2 ; Cut-off for making neighbor
> > list (short range
> > forces)
> > coulombtype = PME ; Treatment of long range
> > electrostatic interactt
> > ions
> > rcoulomb = 1.2 ; long range electrostatic
> > cut-off
> > vdwtype = cutoff
> >
> > 1,1 Top
> >
> > em.log file is
> >
> > Steepest Descents converged to machine precision in 400 steps,
> > but did not reach the requested Fmax < 1000.
> > Potential Energy = -6.1178244e+05
> > Maximum force = 7.0838816e+07 on atom 14616
> > Norm of force = 6.4604380e+05
> >
> > after that i have gone through this and in some cases it can be possible
> > that convergence can not reach the requested force.
> >
> > now i am doing NVT and my NVT.msp is belowed
> > title = Protein-ligand complex NVT equilibration
> > define = -DFLEXIBLE ; position restrain the protein and
> > ligand
> > ; Run parameters
> > integrator = md ; leap-frog integrator
> > dt = 0.002 ; 2 fs
> > nsteps = -1 ; 2 * 5000 = 10 ps
> > ; Output control
> > nstenergy = 10 ; save energies every 1.0 ps
> > nstlog = 10 ; update log file every 1.0 ps
> > nstxout-compressed = 1 ; save coordinates every 1.0 ps
> > energygrps = UNK_JDN Water
> > ; Bond parameters
> > continuation = no ; first dynamics run
> > constraints = all-bonds ; bonds to H are constrained
> > constraint-algorithm = lincs
> > ;shake-tol = 0.0001
> > lincs_order = 8 ; also related to accuracy
> > lincs-iter = 2 ; accuracy of LINCS
> > lincs-warnangle = 10
> > ; Neighbor searching and vdW
> > cutoff-scheme = Verlet
> > coulombtype = PME
> > rcoloumb = 1.0
> > ns_type = grid ; search neighboring grid cells
> > nstlist = 20 ; largely irrelevant with Verlet
> > coulomb-modifier = Potential-shift-Verlet
> > ;nstcomm = 100
> > rlist = 0.9
> > vdwtype = PME
> > vdw-modifier = Potential-shift-Verlet
> > ;rvdw-switch = 1.0
> > rvdw = 1.0 ; short-range van der Waals cutoff
> (in
> > nm)
> > DispCorr = EnerPres
> > ; Electrostatics
> > ;coulombtype = PME ; Particle Mesh Ewald for long-range
> > electrostatics
> > ;rcoulomb = 1.4 ; short-range electrostatic cutoff
> (in
> > nm)
> > pme_order = 8 ; cubic interpolation
> > fourierspacing = 0.16 ; grid spacing for FFT
> > ewald-rtol = 2.5e-5
> > ; Temperature coupling
> > tcoupl = V-rescale ; modified
> > Berendsen thermostat
> > tc-grps = UNK_JDN Water ; two coupling groups - more
> > accurate
> > tau_t = 0.1 0.1 ; time constant,
> in
> > ps
> > ref_t = 300 300
> > nsttcouple = 10 ; reference temperature,
> > one for each group, in K
> > ; Pressure coupling
> > pcoupl = Berendsen ; no pressure coupling in NVT
> > periodic_molecules = no
> > nstpcouple = 20
> > pcoupltype = isotropic
> > tau-p = 3
> > compressibility = 4.5e-5
> > ref-p = 1.0
> > refcoord-scaling = all
> > ; Periodic boundary conditions
> > pbc = xyz ; 3-D PBC
> > ; Dispersion correction is not used for proteins with the C36 additive FF
> > ;DispCorr = no
> > ; Velocity generation
> > gen_vel = no ; assign velocities from Maxwell
> > distribution
> > gen_temp = 300 ; temperature for Maxwell
> distribution
> > gen_seed = -1 ; generate a random seed
> >
> >
> > and i am getting this error
> >
> > Fatal error:
> > Too many LINCS warnings (16238)
> > If you know what you are doing you can adjust the lincs warning threshold
> > in
> > your mdp file
> > or set the environment variable GMX_MAXCONSTRWARN to -1,
> > but normally it is better to fix the problem
> >
> > how can i resolve this error?
> > also in my .log file showing this kind of error
> >
> > Warning: pressure scaling more than 1%, mu: 153.128 153.128 153.128
> > Energies (kJ/mol)
> >
> > how can i control the pressure?
> > thank you in advance.
> >
> > With regards
> > Anjali Patel
> > Research Scholar
> > Department of Physics
> > The M S University of Baroda, Vadodara-390002
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Regards,
Naveen B K
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