Chih-Ying Lin wrote:
Hi
The follwing is my .out file.
From it, can I conclude that some molecule clashing with another ?
No, you can conclude that your system is unstable. One possible reason is
atomic clashing, but you cannot say for sure. General advice on your problem
(which is encountered frequently, and as such, appears thousands of times in the
list archive) can be found on the Gromacs wiki site:
http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
If you want further help, take the advice that I gave you before - look at the
trajectory, focusing specifically on the problematic atoms (looks like 366 and
367 are having problems first, suggesting that either they, or atoms nearby, are
unstable). I also asked about the success of your energy minimization, but you
haven't provided that information. From the output, it seems that your
simulation is crashing immediately, suggesting that EM did not work properly,
and there *may* be unresolved clashes. You will have to do visual inspection to
determine if this is the case.
-Justin
Thank you
Lin
Step -2, time -0.002 (ps) *LINCS WARNING*
relative constraint deviation after LINCS:
max 0.044043 (between atoms 366 and 368) rms 0.001724
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
366 367 36.8 0.1973 0.1301 0.1250
366 368 36.6 0.1963 0.1305 0.1250
starting mdrun 'HEN EGG WHITE LYSOZYME in water'
5000 steps, 5.0 ps.
Step 0, time 0 (ps) *LINCS WARNING
*relative constraint deviation after LINCS:
max 42.623165 (between atoms 1499 and 1518) rms 2.341352
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1376 1377 39.1 0.1470 0.1471 0.1470
1404 1405 59.8 0.1430 0.2374 0.1430
1405 1406 88.5 0.1530 0.2358 0.1530
1406 1407 76.6 0.1530 0.1851 0.1530
1407 1408 74.3 0.1531 0.2407 0.1530
1438 1439 34.8 0.1530 0.1557 0.1530
1439 1440 34.4 0.1530 0.1594 0.1530
1499 1518 90.0 0.1090 4.7549 0.1090
1554 1578 90.0 0.1090 0.2729 0.1090
1594 1595 53.5 0.1390 0.1650 0.1390
1595 1596 57.1 0.1390 0.1515 0.1390
1595 1615 90.3 0.1090 0.5874 0.1090
1666 1652 48.5 0.1392 0.1535 0.1390
1654 1678 90.1 0.1092 0.4554 0.1090
1656 1679 90.2 0.1092 0.1300 0.1090
1657 1680 90.0 0.1092 1.6346 0.1090
1660 1661 58.0 0.1393 0.1424 0.1390
1661 1662 54.5 0.1392 0.1467 0.1390
1661 1681 88.9 0.1091 0.1237 0.1090
1665 1684 89.8 0.1091 0.3454 0.1090
1667 1666 53.1 0.1531 0.1364 0.1530
Back Off! I just backed up step-1.pdb to ./#step-1.pdb.1#
Sorry couldn't backup step-1.pdb to ./#step-1.pdb.2#
Back Off! I just backed up step-1.pdb to ./#step-1.pdb.1#
Back Off! I just backed up 6LYZ-PR.trr to ./#6LYZ-PR.trr.1#
Sorry couldn't backup step-1.pdb to ./#step-1.pdb.2#
Sorry couldn't backup step-1.pdb to ./#step-1.pdb.2#
Back Off! I just backed up step-1.pdb to ./#step-1.pdb.2#
Sorry couldn't backup step-1.pdb to ./#step-1.pdb.2#
Back Off! I just backed up step-1.pdb to ./#step-1.pdb.2#
Sorry couldn't backup step-1.pdb to ./#step-1.pdb.2#
Sorry couldn't backup step-1.pdb to ./#step-1.pdb.2#
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 597108032.000000 (between atoms 366 and 368) rms 26394490.000000
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
26 39 52.0 0.1530 0.1699 0.1530
39 40 69.4 0.1230 0.1423 0.1230
39 41 40.7 0.1330 0.1502 0.1330
75 76 36.0 0.1250 0.1252 0.1250
133 134 69.5 0.1530 0.1937 0.1530
134 135 89.8 0.1470 0.2036 0.1470
344 346 42.4 0.1470 0.2090 0.1470
346 347 42.2 0.1530 0.2141 0.1530
* 346 359 63.9 0.1530 26006.0332 0.1530
359 360 56.9 0.1230 26006.0469 0.1230
359 361 83.2 0.1330 82898.5859 0.1330
361 362 77.5 0.1000 82845.7109 0.1000
361 363 83.8 0.1470 398710.1875 0.1470
363 364 89.3 0.1530 1909291.8750 0.1530
363 369 85.2 0.1530 393002.8125 0.1530
364 365 90.0 0.1508 31146174.0000 0.1530
365 366 90.2 0.1544 66925512.0000 0.1530
366 367 92.7 0.1301 73689816.0000 0.1250
366 368 87.0 0.1305 74638504.0000 0.1250
369 370 72.1 0.1230 65978.3203 0.1230
369 371 72.6 0.1330 66864.2812 0.1330
371 372 85.7 0.1000 10685.0596 0.1000
371 373 61.0 0.1470 10685.1035 0.1470
* 373 374 33.3 0.1530 0.1896 0.1530
373 377 33.5 0.1530 0.1933 0.1530
547 548 90.1 0.1089 0.1358 0.1090
898 900 89.9 0.1530 0.4741 0.1530
1045 1046 47.0 0.1780 0.1783 0.1780
1118 1119 36.8 0.1090 0.1069 0.1090
1128 1129 31.8 0.1000 0.1019 0.1000
1130 1131 35.6 0.1340 0.1334 0.1340
1152 1153 89.6 0.1530 0.2937 0.1530
1153 1154 90.3 0.1529 2.2321 0.1530
1154 1155 89.9 0.1529 7.7561 0.1530
1155 1156 90.3 0.1470 8.2649 0.1470
1156 1157 60.6 0.1000 0.1543 0.1000
1156 1158 49.6 0.1339 0.1783 0.1340
1158 1159 48.4 0.1340 0.1038 0.1340
1159 1160 86.4 0.1000 0.1375 0.1000
1165 1166 45.8 0.1230 0.1207 0.1230
Back Off! I just backed up step-1.pdb to ./#step-1.pdb.3#
Sorry couldn't backup step-1.pdb to ./#step-1.pdb.3#
Back Off! I just backed up step-1.pdb to ./#step-1.pdb.3#
Back Off! I just backed up step-1.pdb to ./#step-1.pdb.4#
Back Off! I just backed up step-1.pdb to ./#step-1.pdb.3#
Back Off! I just backed up step0.pdb to ./#step0.pdb.1#
Back Off! I just backed up step0.pdb to ./#step0.pdb.2#
Wrote pdb files with previous and current coordinates
Back Off! I just backed up step0.pdb to ./#step0.pdb.3#
Wrote pdb files with previous and current coordinates
Back Off! I just backed up step0.pdb to ./#step0.pdb.1#
Sorry couldn't backup step0.pdb to ./#step0.pdb.1#
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Back Off! I just backed up step0.pdb to ./#step0.pdb.1#
Back Off! I just backed up step0.pdb to ./#step0.pdb.4#
Wrote pdb files with previous and current coordinates
Back Off! I just backed up step0.pdb to ./#step0.pdb.5#
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Back Off! I just backed up step0.pdb to ./#step0.pdb.6#
Wrote pdb files with previous and current coordinates
Terminated
Chih-Ying Lin wrote:
>
>
> Hi
> My simulation broke down and the simulation procedues are as follows.
>
> 1. center a protein molecule in the simulation box
> 2. put 20 ligands around the protein with " genbox " command
> 3. make sure that any atom of the ligands does not overlap on any atom
> of the protein with Visulization-software.
> 4. solvent addition , with the command " genbox *-vdwd* 0.2 "
> 5. Addition of ions, with the command " genion "
> 6. Energy minimization of the solvated system
> 7. Position restrained MD
>
> => simulation broke down.
> => It is very probable that some molecule clashing with another.
You can change "probable" to an actual answer if you analyze whatever LINCS
warnings are occurring (the atoms are listed) and by watching the resulting
trajectory.
> => since i have made sured that any atom of the ligands does not overlap
> on any atom of the protein with Visulization-software,
> the clashed pair of the molecules are possible " solvent vs
> solvent " or "solvent vs protein" or "solvent vs
> ligand "
Then you should follow up #4 above with another visual inspection, as
you did
with protein-ligand interactions, in addition to any information printed
to the
log file (as above).
> => however, from the Gromacs manual , command "genbox"
> " Solvent molecules are removed from the box where the distance
> between any atom of the solute molecule(s) and any atom of the solvent
> molecule is less
> than the sum of the VanderWaals radii of both atoms. A database
> (vdwradii.dat <http://manual.gromacs.org/current/online/dat.html>) of
> VanderWaals radii is read by the program, atoms not in the
> database are assigned a default distance -vdw."
>
So solvent-solvent overlap shouldn't be a problem.
> => here is vdwradii.dat (the ligand is simply made of C, N, O, H)
Yes, this is standard.
> ; Very approximate VanderWaals radii
> ; only used for drawing atoms as balls or for calculating atomic overlap.
> ; longest matches are used
> ; '???' or '*' matches any residue name
> ; 'AAA' matches any protein residue name
> ??? C 0.15
> ??? F 0.12
> ??? H 0.04
> ??? N 0.110
> ??? O 0.105
> ??? S 0.16
>
> My questions are
> 1. anything wrong of my simulation procedures ?
In theory, not really. What values of potential energy and maximum
force did
the energy minimization converge to?
> 2. how to find the clashed molecules ?
>
Read the information printed to the log file (again, I'm assuming you're
seeing
LINCS warnings, but you haven't told us what "broke" means!) and watch the
trajectory to see where things start to fall apart. As I suggested to
someone
earlier, if the crash is happening reasonably early, setting "nstxout =
1" is a
useful diagnostic to capture all frames prior to the crash.
-Justin
> Thank you
> Lin
>
>
>
>
>
>
>
--
========================================
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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