[gmx-users] (no subject)

hamedifatemeh67 at yahoo.com hamedifatemeh67 at yahoo.com
Mon Aug 8 13:02:09 CEST 2016


Iam running mdrun and getting 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 andlincs_iter =1 I got above error. I know if we don’t want to deteriorate thelincs accuracy (1+ lincs_iter)*lincs_order has to remain constant. So Idecreased 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 correctit.

 (2)  According to the suggestionsfor trouble shooting of the error, I tried to decrease the number of grid cellsby option –dd but I don’t know what valus I should use with –dd! What is thedifference between –dd 118 and –dd 2 1 4?

           With the first one the run stoppedwhile with the other one it worked.

 (3)  Also I don’t know how can I use–rcon option?!  What value is appropriatefor –rcon?

Thanksin advance for your time


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