[gmx-users] LINCS warning during constrained md

[Mark Abraham]

Hi,

Those are all good things, but have you actually got out a molecular viewer
and looked at the input and output of your resolution conversion?

Mark

On Wed, Jul 12, 2017 at 4:25 PM edesantis <edesantis at roma2.infn.it> wrote:

> Hi,
> thanks for the prompt answer,
>
>
> I've found the same problem even if I try to convert the coarse grained
> pdb obtained from martinize.py, so in that case it should be not a
> problem to have the conversion, for this reason I though it is a
> methodological problem...
>
> I've seen the blowing-up issues , but I think:
> - the timestep is enough small  (0.0002)
> -the system should be enough minimized via the previous steps (in fact
> the sd converged to the machine precision in both cases, actually the
> potential energy is ~10^5, but I don't know how to reduce it, I tried a
> cg after the sd, but the proble is still there)
> -there in not any pressure coupling
> -I've tried a different temperature coupling (berensden, nose-hoover)
> and it doesn't work
> - the md stops at the first step, so there is not any .edr file produced
> to be looked at
>
>
>
> I don't know what else to do...
>
> maybe, do you know another conversion protocol to use??
>
>
> thank you again
> Emiliano
>
> On 2017-07-12 15:11, Mark Abraham wrote:
> > 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
> >>
> >> --
> >> Gromacs Users mailing list
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>
> --
> Emiliano De Santis
> --
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