[gmx-users] LINCS warning during constrained md
mark.j.abraham at gmail.com
Wed Jul 12 15:11:25 CEST 2017
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
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 De Santis
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users