[gmx-users] Problem with domain decomposition

hamedifatemeh67 at yahoo.com hamedifatemeh67 at yahoo.com
Fri Aug 12 07:45:30 CEST 2016


I am running mdrun andgetting following error:

DD cell 0 0 3could only obtain 1065 of the 1066 atoms that are connected via constraintsfrom the neighboring cells. This probably means your constraint lengths are toolong compared to the domain decomposition cell size. Decrease the number ofdomain decomposition grid cells or lincs-order or use the -rcon option ofmdrun.

For solving this problem:

(1) In my mdp file lincs_order = 4 and lincs_iter =1 I got above error. I know if we don’t want to deteriorate the lincs accuracy (1+ lincs_iter)*lincs_order has to remain constant. So I decreased lincs _order to (2) and increased lincs_iter to (3) proportionally. What I am following is right or I have misunderstood it. If so please correct it.
(2) According to the suggestions for trouble shooting of the error, I tried to decrease the number of grid cells by option –dd but I don’t know what valus I should use with –dd! What is the difference between –dd 118 and –dd 2 1 4?           With the first one the run stopped while with the other one it worked.
(3) Also I don’t know how can I use –rcon option?!  What value is appropriate for –rcon?
Thanksin advance for your time


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