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