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On 14/03/2012 9:54 PM, PAVAN PAYGHAN wrote:
<blockquote
cite="mid:CAJ0xtdEHFs-my+iAYkPYtRUN_JJj9hS3f6v4bvLxG_yzGDuxMQ@mail.gmail.com"
type="cite">
<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. <br>
</span></p>
</div>
</blockquote>
<br>
The .log file has a detailed analysis of how DD is setting things
up. You need to make sure that this output is sensible for your
system.<br>
<br>
You should also desist from using P-R pressure coupling during
equilibration (i.e. with velocity generation), as warned in the
manual section on pressure coupling. Perhaps your system is blowing
up.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAJ0xtdEHFs-my+iAYkPYtRUN_JJj9hS3f6v4bvLxG_yzGDuxMQ@mail.gmail.com"
type="cite">
<div>
<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 style="font-family:Arial" lang="FR">pbc
= xyz ;
3-D PBC</span></p>
<p class="MsoNormal"><span style="font-family:Arial" lang="FR">;
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
<br>
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</blockquote>
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