Hi,
I constructed some (about 200 atoms) molecule, have got itp and gro files for
it using PRODRG
server and put it in water box.
Short test run was O'K. But when I tried long run I have got message:
after about 1.5ns time:
----------------------------------------------------------------------------------------------------------
DD cell 0 1 0: Neighboring cells do not have atoms: 73
DD cell 0 3 0: Neighboring cells do not have atoms: 50 49
Program mdrun, VERSION 4.5.5
Source code file: domdec_con.c, line: 693
Fatal error:
DD cell 0 1 0 could only obtain 43 of the 44 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 or use the -rcon option of mdrun. For
more
information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-----------------------------------------------------------------------------------------------------------
I do not know where I can
1) "...decrease the number of domain
decomposition grid cells or
2) decrease lincs-order".
3) I can use -rcon option of mdrun.
In this case I understand how I can change this parameter but I don't know what
are the reasonable values for it.
Is it 0.761A at the beginning of my calculation (see below)?
Should I try to make it shorter or longer?
It looks that from one hand I should make it longer but from another hand it
should be less
than minimum cell size (0.898 in my case? see below)
I have next information about domain decomposition in the beginning of run:
-------------------------------------------------------------------------------------------------------------
Initializing Domain Decomposition on 64 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 0.817 nm, LJ-14, atoms 138 148
multi-body bonded interactions: 0.817 nm, Proper Dih., atoms 148 138
Minimum cell size due to bonded interactions: 0.898 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.761 nm
Estimated maximum distance required for P-LINCS: 0.761 nm
Using 32 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 32 cells with a minimum initial size of 1.123 nm
The maximum allowed number of cells is: X 5 Y 5 Z 5
Domain decomposition grid 4 x 4 x 2, separate PME nodes 32
PME domain decomposition: 4 x 8 x 1
Interleaving PP and PME nodes
This is a particle-particle only node
-------------------------------------------------------------------------------------------------------------
Any ideas what to do?
Thank you in advance.
Alex
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