[gmx-users] LINCS warning during constrained md

edesantis edesantis at roma2.infn.it
Wed Jul 12 15:03:57 CEST 2017

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

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