Dear all,
I am trying to run mdrun. It always prompts the following message and
creates two pdb files stepN.pdb and #stepN.pdb.1# (where N is the step
number) in each step. A stepN.pdb has a TITLE line "one step before crash"
and #stepN-1.pdb.1 has a TITLE "crash". I'd like to know what's wrong in the
run.
The message given in each step is like:
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.003179 (between atoms 41 and 42) rms 0.000636
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
8 9 32.0 0.1000 0.1001 0.1000
41 42 32.0 0.1000 0.1003 0.1000
81 82 31.1 0.1000 0.1002 0.1000
86 87 34.1 0.1000 0.1002 0.1000
103 104 33.1 0.1000 0.1000 0.1000
112 113 52.4 0.1000 0.1002 0.1000
step 0
Step 1, time 0.01 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 1.791684 (between atoms 112 and 113) rms 0.392409
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 84.9 0.1000 0.1038 0.1000
1 3 89.9 0.1000 0.1257 0.1000
1 4 89.9 0.1000 0.1432 0.1000
8 9 89.8 0.1001 0.2546 0.1000
16 17 89.8 0.1001 0.1032 0.1000
25 26 62.7 0.1090 0.1090 0.1090
27 28 53.6 0.1090 0.1090 0.1090
33 34 46.9 0.1000 0.1002 0.1000
41 42 89.8 0.1003 0.2351 0.1000
50 51 89.9 0.1000 0.2237 0.1000
55 56 89.9 0.1000 0.1733 0.1000
60 61 43.5 0.1090 0.1088 0.1090
68 69 89.9 0.1090 0.1182 0.1090
72 73 89.8 0.0999 0.1973 0.1000
81 82 89.8 0.1002 0.2485 0.1000
86 87 89.9 0.1002 0.2528 0.1000
91 92 89.8 0.1090 0.1135 0.1090
93 94 50.0 0.1090 0.1094 0.1090
95 96 89.9 0.1090 0.1674 0.1090
99 100 89.9 0.1090 0.1629 0.1090
103 104 89.8 0.1000 0.2644 0.1000
112 113 89.9 0.1002 0.2792 0.1000
Wrote pdb files with previous and current coordinates
Step 2, time 0.02 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 4.853224 (between atoms 1 and 2) rms 0.722267
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 90.0 0.1038 0.5853 0.1000
1 3 90.0 0.1257 0.4489 0.1000
1 4 90.0 0.1432 0.4522 0.1000
8 9 90.3 0.2546 0.1630 0.1000
16 17 90.2 0.1032 0.1728 0.1000
21 22 51.4 0.1091 0.1112 0.1090
23 24 34.8 0.1093 0.1092 0.1090
25 26 90.0 0.1090 0.2750 0.1090
27 28 89.9 0.1090 0.2709 0.1090
29 30 72.0 0.1092 0.1090 0.1090
33 34 89.9 0.1002 0.2651 0.1000
41 42 35.6 0.2351 0.1006 0.1000
50 51 45.3 0.2237 0.1008 0.1000
55 56 35.2 0.1733 0.1004 0.1000
60 61 89.8 0.1088 0.2472 0.1090
62 63 32.4 0.1092 0.1099 0.1090
64 65 90.0 0.1086 0.2254 0.1090
68 69 90.0 0.1182 0.1829 0.1090
72 73 37.4 0.1973 0.1009 0.1000
81 82 34.7 0.2485 0.1007 0.1000
91 92 90.2 0.1135 0.2354 0.1090
93 94 90.0 0.1094 0.2507 0.1090
95 96 90.2 0.1674 0.1282 0.1090
99 100 89.6 0.1629 0.1165 0.1090
103 104 90.9 0.2644 0.1102 0.1000
112 113 41.3 0.2792 0.1012 0.1000
Back Off! I just backed up step1.pdb to ./#step1.pdb.1#
Wrote pdb files with previous and current coordinates
Step 3, time 0.03 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 4.451822 (between atoms 60 and 61) rms 0.614110
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
21 22 89.9 0.1112 0.2640 0.1090
23 24 90.0 0.1092 0.1886 0.1090
25 26 35.7 0.2750 0.1124 0.1090
27 28 33.7 0.2709 0.1111 0.1090
29 30 89.9 0.1090 0.2706 0.1090
33 34 36.4 0.2651 0.1005 0.1000
41 42 90.0 0.1006 0.2461 0.1000
50 51 90.0 0.1008 0.2485 0.1000
55 56 89.9 0.1004 0.2663 0.1000
60 61 89.8 0.2472 0.5942 0.1090
62 63 89.7 0.1099 0.1401 0.1090
64 65 52.8 0.2254 0.1161 0.1090
66 67 89.7 0.1096 0.1386 0.1090
72 73 90.0 0.1009 0.2522 0.1000
81 82 90.0 0.1007 0.2819 0.1000
86 87 89.9 0.1003 0.3104 0.1000
93 94 90.1 0.2507 0.1387 0.1090
97 98 89.6 0.1081 0.1885 0.1090
103 104 90.0 0.1102 0.1296 0.1000
112 113 90.0 0.1012 0.2632 0.1000
Back Off! I just backed up step2.pdb to ./#step2.pdb.1#
Wrote pdb files with previous and current coordinates
.... ...
Thanks,
George
_________________________________________________________________
Dont just search. Find. Check out the new MSN Search!
http://search.msn.click-url.com/go/onm00200636ave/direct/01/
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
