[gmx-users] cg Fatal error--DD cell

[maggin]

 1)I use steepest  to minimize energy,  .mdp as follows,
title               =  bovin
cpp                 =  /usr/bin/cpp ; the c pre-processor
define              =  -DFLEXIBLE
constraints         =  all-bonds  
integrator          =  steep
dt                  =  0.002	; ps !
nsteps              =  2000
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
coulombtype         =  PME
rcoulomb            =  1.0
vdwtype             =  cut-off
rvdw                =  1.4
fourierspacing        = 0.12
fourier_nx		=  0
fourier_ny		=  0
fourier_nz		=  0
pme_order		=  4
ewald_rtol		=  1e-5
optimize_fft		=  yes
;
;        Energy minimizing stuff
;
emtol               =  1000.0
emstep              =0.01
; GENERATE VELOCITIES FOR STARTUP RUN
gen-vel                  = no
gen-temp                 = 293
gen-seed                 = 173529

2) then I use cg do energy minimization, .mdp as follows,

title               =  bovin
cpp                 =  /usr/bin/cpp
define              =  -DFLEXIBLE
constraints         =  all-bonds
integrator          =  cg
dt                  =  0.002    ; ps !
nsteps              =  1000
nstlist             =  10 
ns_type             =  grid
rlist               =  1.0
coulombtype         =  PME
rcoulomb            =  1.0
vdwtype             =  cut-off
rvdw                =  1.4
fourierspacing                =  0.12
fourier_nx                =  0
fourier_ny                =  0
fourier_nz                =  0
pme_order                =  4
ewald_rtol                =  1e-5
optimize_fft                =  yes
emtol               =  100.0
emstep              =  0.01
; GENERATE VELOCITIES FOR STARTUP RUN
gen-vel                  = no
gen-temp                 = 293
gen-seed                 = 173529

both constraint all bond, 1) steepest is no problem; 
                             but 2)  some error take place at cg
I use 
         grompp_d -f em_cg_constrain.mdp -c em.pdb -p topol.top -o
bovin_em_cg.tpr
         mdrun_d -v -s bovin_em_cg.tpr -deffnm em_cg 
Starting 16 threads,
...........

Fatal error:
DD cell 1 4 0 could only obtain 14 of the 16 atoms that are connected via
constraints from the neighboring cells. This probably means your constraint
lengths are too long compared to the domain decomposition cell size.
Decrease the number of domain decomposition grid cells or lincs-order.

at em_cg.log ,  maximum distance required for P-LINCS: 0.876 nm

So, I revised the mdrun, 
mdrun_d -v -s bovin_em_cg.tpr -deffnm em_cg -nt 2 -rcon 0.876 nm -dds 0.876

another error take place,
Fatal error:
Too many LINCS warnings (1011)
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

So, is anyway to resolve it ?  I have try, but can not find the way.

Thank you very much!

maggin





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