[gmx-users] -rcon parameter in mdrun - what values have sense?

Иимяа Фаамиилиияа aabr at mail.ru
Fri Apr 13 13:39:49 CEST 2012


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.


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