[gmx-users] LINCS warning during constrained md

[Mark Abraham]

Hi,

Sounds like you might be
http://www.gromacs.org/Documentation/Terminology/Blowing_Up because the
conversion doesn't work for your configuration. You should start by doing a
visual check of the configuration for sanity, then follow the advice in
that link.

Mark

On Wed, Jul 12, 2017 at 3:04 PM edesantis <edesantis at roma2.infn.it> wrote:

> dear all,
>
> I am facing a problem with the conversion from Martini CG representation
> to All-atomistic one.
>
> I am using the initram.sh wrapper around the backward.py.
>
> There is a LINCS warning problem when the energy relaxation is performed
> using position restrained md
> (I've also tried to run grompp and mdrun commands directly from the
> terminal and the error persists, so it is not a wrapper problem).
>
> this is the .mdp file generated by the script:
>
> "define                   = -DPOSRES
> integrator               = md
> nsteps                   = 500
> dt                       = 0.0002
> pbc                      = xyz
>
> rcoulomb                 = 0.9
> rlist                    = 0.9
> rvdw                     = 0.9
>
> tcoupl                   = v-rescale
> ref_t                    = 200
> tau_t                    = 0.1
> tc_grps                  = System
>
> gen_vel                  = yes
> gen_temp                 = 300
>
> constraints              = all-bonds "
>
>
> this is the error I found in the .log file:
>
> "Fatal error:
> Too many LINCS warnings (1034)
> 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 "
>
> I tired to comment the constrains part and all is working, but since the
> structure should not be altered too much, I think the constraints are
> required (if I constrain only the h-bonds, it is also working).
>
> I've also added to the .mdp file the lines:
> " lincs-order              = 4 (or 2 or 8)
> lincs-iter               = 1 (or 2 or 10)
> "
> but it is still not working...
>
>
> any of you have suggestions to solve the problem??
> how is it possible to change the environment variable?
>
>
> thanks in advance for your help
> Emiliano
>
> --
> Emiliano De Santis
>
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