I am new to gromacs...please help me and let me know how to proceed..when i give the mdrun command he terminal displays the following:
/usr/local/gromacs/bin/mdrun -nice 0 -v -s hyb2b_vac_md.tpr -o hyb2b_vac_md_1ns_traj.trr -c hyb2b_vac_md_1ns.gro -e hyb2b_vac_md_1ns_ener.edr -g hyb2b_vac_md_1ns.log
:-) G R O M A C S (-:
Grunge ROck MAChoS
:-) VERSION 3.3.1 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2006, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) /usr/local/gromacs/bin/mdrun (-:
Option Filename Type Description
------------------------------------------------------------
-s hyb2b_vac_md.tpr Input Generic run input: tpr tpb tpa xml
-o hyb2b_vac_md_1ns_traj.trr Output Full precision trajectory: trr
trj
-x traj.xtc Output, Opt. Compressed trajectory (portable xdr format)
-c hyb2b_vac_md_1ns.gro Output Generic structure: gro g96 pdb xml
-e hyb2b_vac_md_1ns_ener.edr Output Generic energy: edr ene
-g hyb2b_vac_md_1ns.log Output Log file
-dgdl dgdl.xvg Output, Opt. xvgr/xmgr file
-field field.xvg Output, Opt. xvgr/xmgr file
-table table.xvg Input, Opt. xvgr/xmgr file
-tablep tablep.xvg Input, Opt. xvgr/xmgr file
-rerun rerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb
-tpi tpi.xvg Output, Opt. xvgr/xmgr file
-ei sam.edi Input, Opt. ED sampling input
-eo sam.edo Output, Opt. ED sampling output
-j wham.gct Input, Opt. General coupling stuff
-jo bam.gct Output, Opt. General coupling stuff
-ffout gct.xvg Output, Opt. xvgr/xmgr file
-devout deviatie.xvg Output, Opt. xvgr/xmgr file
-runav runaver.xvg Output, Opt. xvgr/xmgr file
-pi pull.ppa Input, Opt. Pull parameters
-po pullout.ppa Output, Opt. Pull parameters
-pd pull.pdo Output, Opt. Pull data output
-pn pull.ndx Input, Opt. Index file
-mtx nm.mtx Output, Opt. Hessian matrix
-dn dipole.ndx Output, Opt. Index file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 0 Set the nicelevel
-deffnm string Set the default filename for all file options
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-np int 1 Number of nodes, must be the same as used for
grompp
-nt int 1 Number of threads to start on each node
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]sepdvdl bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-[no]multi bool no Do multiple simulations in parallel (only with
-np > 1)
-replex int 0 Attempt replica exchange every # steps
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]glas bool no Do glass simulation with special long range
corrections
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system
Back Off! I just backed up hyb2b_vac_md_1ns.log to ./#hyb2b_vac_md_1ns.log.1#
Getting Loaded...
Reading file hyb2b_vac_md.tpr, VERSION 3.3.1 (single precision)
Loaded with Money
starting mdrun 'DRG'
400000 steps, 1000.0 ps.
step 156610, will finish at Tue Nov 14 11:36:08 2006
Step 156619, time 391.547 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 1.235368 (between atoms 9 and 16) rms 0.131218
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
7 9 45.3 0.1470 0.1738 0.1470
9 16 82.0 0.1326 0.2973 0.1330
10 11 32.8 0.1530 0.1828 0.1530
16 17 89.9 0.1226 0.1771 0.1230
16 18 84.2 0.1541 0.2315 0.1530
18 19 33.7 0.1470 0.1792 0.1470
Wrote pdb files with previous and current coordinates
Step 156620, time 391.55 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 7.148781 (between atoms 9 and 10) rms 0.983396
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
7 9 88.7 0.1738 0.4815 0.1470
9 10 92.9 0.1596 1.1979 0.1470
9 16 128.5 0.2973 0.4633 0.1330
10 11 87.8 0.1828 0.9363 0.1530
11 12 35.9 0.1280 0.1537 0.1230
13 15 32.1 0.1008 0.1164 0.1000
16 17 109.7 0.1771 0.8290 0.1230
16 18 156.9 0.2315 0.1646 0.1530
18 19 102.6 0.1792 0.1550 0.1470
24 25 31.7 0.1301 0.1346 0.1230
Back Off! I just backed up step156619.pdb to ./#step156619.pdb.1#
Wrote pdb files with previous and current coordinates
step 156620, will finish at Tue Nov 14 11:36:11 2006Warning: 1-4 interaction between 7 and 17 at distance 1.011 which is larger than the 1-4 table size 1.000 nmThese 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
Step 156621, time 391.552 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 12.247591 (between atoms 9 and 16) rms 1.513366
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 39.2 0.1386 0.1675 0.1390
1 6 113.5 0.1403 0.0654 0.1390
4 5 33.6 0.1382 0.1725 0.1390
5 6 96.3 0.1412 0.0713 0.1390
7 8 114.2 0.1624 0.2766 0.1530
7 9 153.7 0.4814 0.9763 0.1470
9 10 138.1 1.1977 0.8364 0.1470
9 16 109.0 0.4632 1.7619 0.1330
10 11 131.9 0.9361 0.5693 0.1530
11 12 80.0 0.1536 0.6929 0.1230
11 13 86.6 0.1523 0.6955 0.1330
13 14 94.6 0.1088 0.3135 0.1000
13 15 63.0 0.1164 0.1204 0.1000
16 17 89.0 0.8288 0.5757 0.1230
16 18 151.6 0.1646 0.5035 0.1530
18 19 134.6 0.1550 0.2206 0.1470
19 20 106.4 0.1745 0.4050 0.1470
19 24 108.6 0.1639 0.4129 0.1330
20 21 33.2 0.1613 0.1457 0.1530
20 22 55.4 0.1634 0.1288 0.1530
22 23 30.6 0.1552 0.1755 0.1530
24 25 65.8 0.1345 0.1296 0.1230
Back Off! I just backed up step156620.pdb to ./#step156620.pdb.1#
Wrote pdb files with previous and current coordinates
Step 156622, time 391.555 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 156.416000 (between atoms 27 and 28) rms 43.887146
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 155.9 0.1679 1.3713 0.1390
1 6 165.9 0.0656 5.7379 0.1390
2 3 89.1 0.1437 0.4223 0.1390
3 4 89.4 0.1416 0.3068 0.1390
4 5 139.8 0.1730 1.2976 0.1390
5 6 169.0 0.0715 5.8196 0.1390
6 7 163.1 0.5102 13.7829 0.1530
7 8 147.6 0.2774 10.9817 0.1530
7 9 160.5 0.9791 16.5650 0.1470
9 10 170.4 0.8388 12.9173 0.1470
9 16 157.1 1.7670 18.6046 0.1330
10 11 160.5 0.5710 9.0364 0.1530
11 12 170.7 0.6950 4.6000 0.1230
11 13 170.8 0.6975 4.7046 0.1330
13 14 77.3 0.3144 1.5544 0.1000
13 15 51.3 0.1208 1.6563 0.1000
16 17 110.0 0.5774 15.5720 0.1230
16 18 118.9 0.5049 15.9163 0.1530
18 19 55.9 0.2213 17.6087 0.1470
19 20 56.9 0.4062 22.6568 0.1470
22 23 132.0 0.1760 1.8040 0.1530
24 26 44.3 0.1084 18.9838 0.1530
26 27 115.3 0.1651 16.6028 0.1470
27 28 78.8 0.1540 23.1402 0.1470
27 36 81.3 0.1423 20.7586 0.1330
28 29 109.2 0.1587 7.2465 0.1530
29 30 103.3 0.1536 3.7558 0.1530
30 31 50.5 0.1524 1.3613 0.1530
31 32 110.6 0.1476 0.1332 0.1470
32 33 65.6 0.1002 0.3047 0.1000
32 34 72.2 0.1003 0.3269 0.1000
32 35 66.0 0.1002 0.3122 0.1000
36 37 91.3 0.1264 8.1830 0.1230
36 38 90.4 0.1562 7.6206 0.1530
38 39 85.9 0.1482 6.8321 0.1470
39 40 72.5 0.1476 0.8344 0.1470
39 48 69.1 0.1337 0.9899 0.1330
40 41 79.8 0.1535 0.4217 0.1530
40 42 79.3 0.1535 0.4262 0.1530
42 43 42.2 0.1394 0.1974 0.1390
42 47 42.6 0.1394 0.1979 0.1390
48 49 68.0 0.1234 0.3369 0.1230
48 50 71.2 0.1535 0.4167 0.1530
50 51 58.0 0.1475 0.2531 0.1470
Back Off! I just backed up step156621.pdb to ./#step156621.pdb.1#
Wrote pdb files with previous and current coordinates
Step 156623 Warning: pressure scaling more than 1%, mu: 3.98712 3.98712 3.98712
Step 156623, time 391.557 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 3.089954 (between atoms 98 and 100) rms nan
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
61 62 34.3 0.1539 0.1918 0.1530
70 71 58.7 0.1479 0.2698 0.1470
96 97 36.3 0.1006 0.0909 0.1000
96 98 88.0 0.1338 0.3737 0.1330
98 99 88.8 0.1539 0.3097 0.1530
98 100 89.2 0.1237 0.5031 0.1230
Back Off! I just backed up step156622.pdb to ./#step156622.pdb.1#
Wrote pdb files with previous and current coordinates
-------------------------------------------------------
Program mdrun, VERSION 3.3.1
Source code file: nsgrid.c, line: 220
Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.
-------------------------------------------------------
"I'm Gonna Get Medieval On Your Ass" (Pulp Fiction)
What is wrong and what should be done.
redgards
nur
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