[gmx-users] LINCS warnings (6153)

Vishwanath Dalvi vishwanathhdalvi at yahoo.co.in
Thu May 28 21:00:27 CEST 2009


I had the same problem and this is what worked for me:
1.  You must do an equilibration run WITHOUT any constraints (replace constrained bonds with harmonic bonds (equilibrium bond length = constraint length and force constant suitably high) and increase weight of H atoms to 10.0.
2.  Do an equilibration run ( 1ns if practical) with this system.
3.  Use the confout.gro file it generates to start your run WITH constraints and the canonical H atom weights.

This should work.


From: Ernesto Andres Román <indio18 at hotmail.com>
To: gmx-users at gromacs.org
Sent: Thursday, 28 May, 2009 1:10:54 PM
Subject: [gmx-users] LINCS warnings (6153)

 Dear gmx-user,
                           Im just making my first moves in protein dynamics simulation. Ive done some tutorials and peptide-water simulations. But now im intending to change the solvent to CCL4. Ive got the solvent parameters, made the topology file, and the .gro file with the solvent and peptide together. When I run mdrun commando an error message displays:
Fatal error:
Too many LINCS warnings (6153)
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

My .mdp file is:
define              = -DFLEXIBLE
constraints         = none
integrator          = steep
dt                  = 0.002     ; ps !
nsteps              = 400
nstlist             = 10
ns_type             = grid
rlist               = 1.0
coulombtype         = PME
rcoulomb            = 1.0
vdwtype             = cut-off
rvdw                = 1.4
fourierspacing          = 0.12
fourier_nx        = 0
fourier_ny        = 0
fourier_nz        = 0
pme_order         = 4
ewald_rtol        = 1e-5
optimize_fft            = yes
;       Energy minimizing stuff
emtol               = 1000.0
emstep              = 0.01

Do you know what could be happening, and more important, how to solve it or where to look for the problem ?

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