ansu...@physics.iisc.ernet.in wrote:
dear gmx-users,
i am getting the following error message while running production md
(mpirun)......
Step 102, time 0.204 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 122.760095, max 2890.435059 (between atoms 5092 and 5090)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
5079 5069 30.7 0.1532 0.1888 0.1522
5081 5079 79.8 0.1056 0.2608 0.1335
5080 5079 39.1 0.1237 0.1673 0.1229
5083 5081 79.7 0.1459 0.8597 0.1449
5082 5081 78.7 0.1016 0.1856 0.1010
5098 5083 78.5 0.1532 0.7685 0.1522
5085 5083 85.9 0.1537 1.9840 0.1526
5084 5083 70.4 0.1097 0.4235 0.1090
5088 5085 83.6 0.1536 2.4114 0.1526
5087 5085 85.9 0.1098 1.5565 0.1090
5086 5085 87.3 0.1099 1.2617 0.1090
5088 5094 88.6 0.1535 3.0328 0.1526
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Warning: 1-4 interaction between 5093 and 5094 at distance 6.570 which is
larger than the 1-4 table size 2.200 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Warning: 1-4 interaction between 5091 and 5094 at distance 2.444 which is
larger than the 1-4 table size 2.200 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Fatal error:
1 particles communicated to PME node 3 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.
any suggestion to get rid of this problem........
Please search the Gromacs website, where this issue is discussed in some depth,
and/or search the list archive to find any of the thousands of posts where this
issue has been solved before.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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