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On 15/03/2012 5:36 PM, PAVAN PAYGHAN wrote:
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On 14/03/2012 9:54 PM, PAVAN PAYGHAN wrote:<br>
><br>
> Dear Gromacs Users,<br>
><br>
> I am running mdrun on single node with 8 CPU and getting
following error<br>
><br>
> Fatal error:-<br>
><br>
> D D cell 1 0 0 could only obtain 1520 of the 1521 atoms
that are<br>
> connected via constraints from the neighbouring cells.<br>
><br>
> This probably means your constraint length are too long
compared to<br>
> the domain decomposition cell size.<br>
><br>
> Decrease the number of domain decomposition grid cells or
lincs order.<br>
><br>
<br>
The .log file has a detailed analysis of how DD is setting
things up.<br>
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<br>
equilibration (i.e. with velocity generation), as warned in
the manual<br>
section on pressure coupling. Perhaps your system is blowing
up.<br>
<br>
Mark<br>
<br>
</blockquote>
<div> Dear Mark,</div>
<div><br>
</div>
<div>Thanks for the reply.</div>
<div> I have successfully done the equilibration run ,while
doing production run I am gettiing above error (almost after
10 ns run).</div>
<div> Also It would be worth working if you explain the
importance -rcon value and other things that I have asked .</div>
</div>
</blockquote>
<br>
A description of your system, GROMACS version and objective are
important to solving the problem. I don't think we've seen those.
Nobody wants to spend time talking about DD options if you are
trying to run a system with 1000 atoms on 8 processors. By not
describing fully, you make it easy for people to not be bothered.<br>
<br>
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<div>Regards,</div>
<div><br>
</div>
<div>Pavan</div>
<div><br>
</div>
<div> </div>
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> For solving this problem following are the attempts by
me.<br>
><br>
> *1] Decreasing grid cell size:-*<br>
><br>
> As per the suggestion in error, I tried to decrease the
grid cells by<br>
> option -dd from 8 1 1 to 6 1 1 , it has thrown following
error..<br>
><br>
> Fatal error:-The size of the DD grid (6) does not match
the number of<br>
> nodes(8).<br>
><br>
> Can you please suggest any better way to overcome this
for decreasing<br>
> grid cell size.<br>
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<br>
You can't decrease the number of DD cells since you need one per
processor. Maybe you are trying to parallelize a system that is too
small for this number of processors, which brings us back to needing
a description of your system.<br>
<br>
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><br>
> *2] -rcon option:*<br>
><br>
> What is the correlation between the -rcon value with DD
cell<br>
> size(Directly or inversely proportional ) , for the
problem entitled<br>
> above what should be the strategy (to decrease or to
increase rcon value).<br>
><br>
> If one changes the -rcon value will it affect the lincs
accuracy, or<br>
> in other words the run will hold the same continuation or
any change<br>
> in it.<br>
><br>
> For changing the -rcon value the reference of previous
log file i.e.<br>
> Estimated maximum distance required for p-lincs say
0.877, so one can<br>
> increase than what has been estimated.<br>
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</div>
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<br>
You need to read mdrun -h about -rcon. You need to be trying to
increase the ratio of cell size to constraint length, per the error
message.<br>
<br>
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><br>
> *3] lincs_order and lincs_iter :*<br>
><br>
> **<br>
><br>
> If we don't want to deteriorate the lincs accuracy (1+<br>
> lincs_iter)*lincs_order has to remain constant , In my
case<br>
><br>
> With lincs_order = 4 and lincs_iter =1 I got above error.
So I<br>
> decreased lincs _order (2) and increased lincs_iter(3)
proportionally.<br>
> What I am following is right or I have misunderstood it.
If so please<br>
> correct it. Can this value be fraction?<br>
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<br>
The values must be integers.<br>
<br>
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> Values which I have tried are relevant or very bad?**<br>
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<br>
That is a correct approach for maintaining LINCS accuracy and trying
to decrease the required constraint length, however it may not help
solve the underlying problem. <br>
<br>
Mark<br>
<br>
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><br>
> Please explain it.<br>
><br>
> If the same problem can be solved by any other
methodology please<br>
> explain it.<br>
><br>
> *Please see the mdp file details.*<br>
><br>
><br>
> integrator = md<br>
><br>
> nsteps = 10000000<br>
><br>
> dt = 0.002 ; 2
fs<br>
><br>
> ; Output control<br>
><br>
> nstxout = 1000
; save<br>
> coordinates every 2 ps<br>
><br>
> nstvout = 1000
; save<br>
> velocities every 2 ps<br>
><br>
> nstxtcout = 1000 ; xtc
compressed<br>
> trajectory output every 2 ps<br>
><br>
> nstenergy = 1000 ; save
energies every 2 ps<br>
><br>
> nstlog = 1000 ;
update log file<br>
> every 2 ps<br>
><br>
> ; Bond parameters<br>
><br>
> continuation = yes ; Restarting after
NPT<br>
><br>
> constraint_algorithm = lincs ; holonomic constraints<br>
><br>
> constraints = all-bonds ; all bonds (even
heavy atom-H<br>
> bonds)<br>
><br>
> lincs_iter = 1 ;
accuracy of LINCS<br>
><br>
> lincs_order = 4<br>
><br>
> ; Neighborsearching<br>
><br>
> ns_type = grid<br>
><br>
> nstlist = 5<br>
><br>
> rlist = 1.2<br>
><br>
> rcoulomb = 1.2<br>
><br>
> rvdw = 1.2<br>
><br>
> ; Electrostatics<br>
><br>
> coulombtype = PME<br>
><br>
> pme_order = 4<br>
><br>
> fourierspacing = 0.16<br>
><br>
> ; Temperature coupling is on<br>
><br>
> tcoupl = Nose-Hoover<br>
><br>
> tc-grps = Protein P SOL_NA_CL
; three<br>
> coupling groups - more accurate<br>
><br>
> tau_t = 0.5 0.5 0.5<br>
><br>
> ref_t = 323 323 323<br>
><br>
> group, in K<br>
><br>
> ; Pressure coupling is on<br>
><br>
> pcoupl = Parrinello-Rahman ; Pressure
coupling on in NPT<br>
><br>
> pcoupltype = semiisotropic ;
uniform<br>
> scaling of x-y box vectors, independent z<br>
><br>
> tau_p = 2.0
; time<br>
> constant, in ps<br>
><br>
> ref_p = 1.0 1.0
; reference<br>
> pressure, x-y, z (in bar)<br>
><br>
> compressibility = 4.5e-5 4.5e-5 ; isothermal
compressibility, bar^-1<br>
><br>
> ; Periodic boundary conditions<br>
><br>
> pbc = xyz ;
3-D PBC<br>
><br>
> ; Dispersion correction<br>
><br>
> DispCorr = EnerPres ; account for cut-off vdW
scheme<br>
><br>
> ; Velocity generation<br>
><br>
> gen_vel = yes<br>
><br>
> **<br>
><br>
> Pavan<br>
><br>
><br>
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