[gmx-users] Infinite polymer, pbc=full and LINCS

Malin Bergenstråhle malbe at kth.se
Thu Nov 17 10:41:05 CET 2005


I am simulating a system of infinite polymer chains using pbc=full and LINCS bond constraints. 
My system is unreliable and sometimes the simulations crash due to LINCS complaining about too large bond rotations. 
I have now noted that it seems like LINCS gives warnings of the kind:

Step 22525, time 67.575 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.000029 (between atoms 22 and 23) rms 0.000004
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    347    348   30.6    0.1000   0.1000      0.1000

and the atoms are always situated on different sides of a periodic bound. A question that now arises is whether this could be a bug with pbc=full or whether there is a problem with my system. I am using  Gromacs 3.3.

Any suggestions about how I could check this or whatever about whatever the problem could be I would be grateful.

Best regards,


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