<div><p class="MsoNormal"><span style="font-family:Arial">Dear Gromacs
Users,</span></p>
<p class="MsoNormal"><span style="font-family:Arial"> </span></p>
<p class="MsoNormal"><span style="font-family:Arial">I am running
mdrun on single node with 8 CPU and getting following error</span></p>
<p class="MsoNormal"><span style="font-family:Arial">Fatal error:-</span></p>
<p class="MsoNormal"><span style="font-family:Arial">D D cell 1
0 0 could only obtain 1520 of the 1521 atoms that are connected via constraints
from the neighbouring cells.</span></p><p class="MsoNormal"><span style="font-family:Arial">This probably means your constraint length are too
long compared to the domain decomposition cell size. </span></p>
<p class="MsoNormal"><span style="font-family:Arial">Decrease the
number of domain decomposition grid cells or lincs order. </span></p>
<p class="MsoNormal"><span style="font-family:Arial"> </span></p>
<p class="MsoNormal"><span style="font-family:Arial"> </span></p>
<p class="MsoNormal"><span style="font-family:Arial">For solving this
problem following are the attempts by me.</span></p>
<p class="MsoNormal"><span style="font-family:Arial"> </span></p>
<p class="MsoNormal"><b><span style="font-family:Arial">1] Decreasing
grid cell size:-</span></b></p>
<p class="MsoNormal"><span style="font-family:Arial"> </span></p>
<p class="MsoNormal"><span style="font-family:Arial"> As per the
suggestion in error, I tried to decrease the grid cells by option -dd from 8 1
1 to 6 1 1 , it has thrown following error..</span></p>
<p class="MsoNormal"><span style="font-family:Arial"> Fatal
error:-The size of the DD grid (6) does not match the number of nodes(8).</span></p>
<p class="MsoNormal"><span style="font-family:Arial"> </span></p>
<p class="MsoNormal"><span style="font-family:Arial">Can you please
suggest any better way to overcome this for decreasing grid cell size.</span></p>
<p class="MsoNormal"><span style="font-family:Arial"> </span></p>
<p class="MsoNormal"><b><span style="font-family:Arial">2] -rcon
option:</span></b><span style="font-family:Arial"></span></p>
<p class="MsoNormal"><span style="font-family:Arial"> </span></p>
<p class="MsoNormal"><span style="font-family:Arial">What is the
correlation between the -rcon value with DD cell size(Directly or inversely
proportional ) , for the problem entitled above what should be
the strategy (to decrease or to increase rcon value).</span></p>
<p class="MsoNormal"><span style="font-family:Arial">If one changes
the -rcon value will it affect the lincs accuracy, or in other words the run
will hold the same continuation or any change in it.</span></p>
<p class="MsoNormal"><span style="font-family:Arial">For changing the
-rcon value the reference of previous log file i.e. Estimated maximum distance
required for p-lincs say 0.877, so one can increase than what has been
estimated.</span></p>
<p class="MsoNormal"><span style="font-family:Arial"> </span></p>
<p class="MsoNormal"><b><span style="font-family:Arial">3] lincs_order and lincs_iter :</span></b></p>
<p class="MsoNormal"><b><span style="font-family:Arial"> </span></b></p>
<p class="MsoNormal"><span style="font-family:Arial">If we don’t want
to deteriorate the lincs accuracy (1+ lincs_iter)*lincs_order has to remain
constant , In my case </span></p>
<p class="MsoNormal"><span style="font-family:Arial">With lincs_order
= 4 and lincs_iter =1 I got above error. So I decreased lincs _order (2) and
increased lincs_iter(3) proportionally. What I am following is right or I have
misunderstood it. If so please correct it. Can this value be fraction?</span></p>
<p class="MsoNormal"><span style="font-family:Arial">Values which I
have tried are relevant or very bad?<b> </b></span></p>
<p class="MsoNormal"><span style="font-family:Arial">Please explain
it.</span></p>
<p class="MsoNormal"><span style="font-family:Arial"> </span></p>
<p class="MsoNormal"><span style="font-family:Arial">If the same
problem can be solved by any other methodology please explain it.</span></p>
<p class="MsoNormal"><span style="font-family:Arial"> </span></p>
<p class="MsoNormal"><span style="font-family:Arial"> </span></p>
<p class="MsoNormal"><b>Please see the mdp
file details.</b></p>
<p class="MsoNormal"><span style="font-family:Arial"><br></span></p><p class="MsoNormal"><span style="font-family:Arial">integrator = md </span></p>
<p class="MsoNormal"><span style="font-family:Arial">nsteps = 10000000 </span></p>
<p class="MsoNormal"><span style="font-family:Arial">dt = 0.002 ;
2 fs</span></p>
<p class="MsoNormal"><span style="font-family:Arial">; Output control</span></p>
<p class="MsoNormal"><span style="font-family:Arial">nstxout = 1000 ; save coordinates every
2 ps</span></p>
<p class="MsoNormal"><span style="font-family:Arial">nstvout = 1000 ; save velocities every
2 ps</span></p>
<p class="MsoNormal"><span style="font-family:Arial">nstxtcout = 1000 ;
xtc compressed trajectory output every 2 ps</span></p>
<p class="MsoNormal"><span style="font-family:Arial">nstenergy = 1000 ;
save energies every 2 ps</span></p>
<p class="MsoNormal"><span style="font-family:Arial">nstlog = 1000 ; update log file every 2 ps</span></p>
<p class="MsoNormal"><span style="font-family:Arial">; Bond
parameters</span></p>
<p class="MsoNormal"><span style="font-family:Arial">continuation = yes ; Restarting after NPT </span></p>
<p class="MsoNormal"><span style="font-family:Arial">constraint_algorithm
= lincs ; holonomic constraints </span></p>
<p class="MsoNormal"><span style="font-family:Arial">constraints = all-bonds ; all bonds (even heavy atom-H bonds) </span></p>
<p class="MsoNormal"><span style="font-family:Arial">lincs_iter = 1 ; accuracy of LINCS</span></p>
<p class="MsoNormal"><span style="font-family:Arial">lincs_order = 4 </span></p>
<p class="MsoNormal"><span style="font-family:Arial">;
Neighborsearching </span></p>
<p class="MsoNormal"><span style="font-family:Arial">ns_type = grid </span></p>
<p class="MsoNormal"><span style="font-family:Arial">nstlist = 5 </span></p>
<p class="MsoNormal"><span style="font-family:Arial">rlist = 1.2 </span></p>
<p class="MsoNormal"><span style="font-family:Arial">rcoulomb = 1.2 </span></p>
<p class="MsoNormal"><span style="font-family:Arial">rvdw = 1.2 </span></p>
<p class="MsoNormal"><span style="font-family:Arial">; Electrostatics</span></p>
<p class="MsoNormal"><span style="font-family:Arial">coulombtype = PME </span></p>
<p class="MsoNormal"><span style="font-family:Arial">pme_order = 4 </span></p>
<p class="MsoNormal"><span style="font-family:Arial">fourierspacing = 0.16 </span></p>
<p class="MsoNormal"><span style="font-family:Arial">; Temperature
coupling is on</span></p>
<p class="MsoNormal"><span style="font-family:Arial">tcoupl = Nose-Hoover </span></p>
<p class="MsoNormal"><span style="font-family:Arial">tc-grps = Protein P SOL_NA_CL ; three coupling groups - more accurate</span></p>
<p class="MsoNormal"><span style="font-family:Arial">tau_t = 0.5 0.5 0.5
</span></p>
<p class="MsoNormal"><span style="font-family:Arial">ref_t = 323 323 323 </span></p>
<p class="MsoNormal"><span style="font-family:Arial">group, in K</span></p>
<p class="MsoNormal"><span style="font-family:Arial">; Pressure
coupling is on</span></p>
<p class="MsoNormal"><span style="font-family:Arial">pcoupl = Parrinello-Rahman ;
Pressure coupling on in NPT</span></p>
<p class="MsoNormal"><span style="font-family:Arial">pcoupltype = semiisotropic ;
uniform scaling of x-y box vectors, independent z</span></p>
<p class="MsoNormal"><span style="font-family:Arial">tau_p = 2.0
; time constant, in ps</span></p>
<p class="MsoNormal"><span style="font-family:Arial">ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar)</span></p>
<p class="MsoNormal"><span style="font-family:Arial">compressibility
= 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1</span></p>
<p class="MsoNormal"><span style="font-family:Arial">; Periodic
boundary conditions</span></p>
<p class="MsoNormal"><span lang="FR" style="font-family:Arial">pbc = xyz ;
3-D PBC</span></p>
<p class="MsoNormal"><span lang="FR" style="font-family:Arial">; Dispersion correction</span></p>
<p class="MsoNormal"><span style="font-family:Arial">DispCorr = EnerPres ; account for cut-off vdW scheme</span></p>
<p class="MsoNormal"><span style="font-family:Arial">; Velocity
generation</span></p>
<p class="MsoNormal"><span style="font-family:Arial">gen_vel = yes </span></p>
<p class="MsoNormal"><b> </b></p></div>Pavan