[gmx-users] Lincs warning_set GMX_MAXCONSTRWARN to -1

[Mark Abraham]

Hi,

The problem is often not anything to do with how you used GROMACS. If your
input structure has a big pocket of vacuum then atoms will go flying across
it and be unhappy. Likewise if a water is too close to a solute atom. Only
you can visualize your structures and see such things.

Mark

On Sun, 7 Apr 2019 at 12:09, Anjali Patel <anjalipatel60316 at gmail.com>
wrote:

> @Mark Abraham
>  Thank you for your kind suggestion. I have checked all structures. After
> the minimization eater molecules got close. i have changed all possible
> input parameters. still got the same error can you please help to point out
> where i am wrong? Here, i have used spc.itp and tip3p.itp of gromos53a5.ff.
> i attaching my em.mdp file.
> em.mdp
> ; 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               = 1400.0    ; Stop minimization when the maximum force
> < 10.0 kJ/mol
> emstep          = 0.001      ; Energy step size
> nsteps              = 50000             ; Maximum number of (minimization)
> steps to perform
> ;nbfgscorr         = 10
> ;constraints       = none
> ;lincs-order       = 8
> ; 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
> cutoff-scheme   = Verlet
> ewald_rtol      = 1e-6
> ns_type             = grid                  ; Method to determine neighbor
> list (simple, grid)
> rlist               = 1.2                   ; Cut-off for making neighbor
> list (short range forces)
> coulombtype         = PME                   ; Treatment of long range
> electrostatic interactions
> rcoulomb            = 1.2                   ; long range electrostatic
> cut-off
> vdwtype         = PME
> vdw-modifier    = Potential-shift
> rvdw-switch     = 1.0
> rvdw                = 1.2                   ; long range Van der Waals
> cut-off
> pbc             = xyz               ; Periodic Boundary Conditions
> DispCorr        = no
>
>
>
> With regards
> Anjali Patel
> Research Scholar
> Department of Physics
> The M S University of Baroda, Vadodara-390002
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