Dear All<br> 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:<br> <br> /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<br> :-) G R O M A C S (-:<br> <br> Grunge ROck MAChoS<br> <br> :-) VERSION 3.3.1 (-:<br> <br> <br>
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br> Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br> Copyright (c) 2001-2006, The GROMACS development team,<br> check out http://www.gromacs.org for more information.<br> <br> This program is free software; you can redistribute it and/or<br> modify it under the terms of the GNU General Public License<br> as published by the Free Software Foundation; either version 2<br> of the License, or (at your option) any later version.<br> <br>
:-) /usr/local/gromacs/bin/mdrun (-:<br> <br> Option Filename Type Description<br> ------------------------------------------------------------<br> -s hyb2b_vac_md.tpr Input Generic run input: tpr tpb tpa xml<br> -o hyb2b_vac_md_1ns_traj.trr Output Full precision trajectory: trr<br> trj<br> -x traj.xtc Output, Opt. Compressed trajectory (portable xdr format)<br> -c hyb2b_vac_md_1ns.gro
Output Generic structure: gro g96 pdb xml<br> -e hyb2b_vac_md_1ns_ener.edr Output Generic energy: edr ene<br> -g hyb2b_vac_md_1ns.log Output Log file<br> -dgdl dgdl.xvg Output, Opt. xvgr/xmgr file<br> -field field.xvg Output, Opt. xvgr/xmgr file<br> -table table.xvg Input, Opt. xvgr/xmgr file<br> -tablep tablep.xvg Input, Opt. xvgr/xmgr file<br> -rerun rerun.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb<br> -tpi tpi.xvg Output, Opt. xvgr/xmgr file<br> -ei sam.edi Input, Opt. ED sampling input<br> -eo sam.edo Output, Opt. ED sampling
output<br> -j wham.gct Input, Opt. General coupling stuff<br> -jo bam.gct Output, Opt. General coupling stuff<br> -ffout gct.xvg Output, Opt. xvgr/xmgr file<br> -devout deviatie.xvg Output, Opt. xvgr/xmgr file<br> -runav runaver.xvg Output, Opt. xvgr/xmgr file<br> -pi pull.ppa Input, Opt. Pull parameters<br> -po pullout.ppa Output, Opt. Pull parameters<br> -pd pull.pdo Output, Opt. Pull data output<br> -pn pull.ndx Input, Opt. Index file<br> -mtx nm.mtx Output, Opt. Hessian matrix<br> -dn dipole.ndx Output, Opt. Index file<br>
<br> Option Type Value Description<br> ------------------------------------------------------<br> -[no]h bool no Print help info and quit<br> -[no]X bool no Use dialog box GUI to edit command line options<br> -nice int 0 Set the nicelevel<br> -deffnm string Set the default filename for all file options<br> -[no]xvgr bool yes Add specific codes (legends etc.) in the output<br> xvg files for the xmgrace
program<br> -np int 1 Number of nodes, must be the same as used for<br> grompp<br> -nt int 1 Number of threads to start on each node<br> -[no]v bool yes Be loud and noisy<br> -[no]compact bool yes Write a compact log file<br> -[no]sepdvdl bool no Write separate V and dVdl terms for each<br> interaction type
and node to the log file(s)<br> -[no]multi bool no Do multiple simulations in parallel (only with<br> -np > 1)<br> -replex int 0 Attempt replica exchange every # steps<br> -reseed int -1 Seed for replica exchange, -1 is generate a seed<br> -[no]glas bool no Do glass simulation with special long range<br> corrections<br> -[no]ionize bool no Do a
simulation including the effect of an X-Ray<br> bombardment on your system<br> <br> <br> Back Off! I just backed up hyb2b_vac_md_1ns.log to ./#hyb2b_vac_md_1ns.log.1#<br> Getting Loaded...<br> Reading file hyb2b_vac_md.tpr, VERSION 3.3.1 (single precision)<br> Loaded with Money<br> <br> starting mdrun 'DRG'<br> 400000 steps, 1000.0 ps.<br> <br> step 156610, will finish at Tue Nov 14 11:36:08 2006<br> Step 156619, time 391.547 (ps) LINCS WARNING<br> relative constraint deviation after LINCS:<br> max 1.235368 (between atoms 9 and 16) rms 0.131218<br> bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 7 9 45.3 0.1470
0.1738 0.1470<br> 9 16 82.0 0.1326 0.2973 0.1330<br> 10 11 32.8 0.1530 0.1828 0.1530<br> 16 17 89.9 0.1226 0.1771 0.1230<br> 16 18 84.2 0.1541 0.2315 0.1530<br> 18 19 33.7 0.1470 0.1792 0.1470<br> Wrote pdb files with previous and current coordinates<br> <br> Step 156620, time 391.55 (ps) LINCS WARNING<br> relative constraint deviation
after LINCS:<br> max 7.148781 (between atoms 9 and 10) rms 0.983396<br> bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 7 9 88.7 0.1738 0.4815 0.1470<br> 9 10 92.9 0.1596 1.1979 0.1470<br> 9 16 128.5 0.2973 0.4633 0.1330<br> 10 11 87.8 0.1828 0.9363 0.1530<br> 11 12 35.9 0.1280 0.1537
0.1230<br> 13 15 32.1 0.1008 0.1164 0.1000<br> 16 17 109.7 0.1771 0.8290 0.1230<br> 16 18 156.9 0.2315 0.1646 0.1530<br> 18 19 102.6 0.1792 0.1550 0.1470<br> 24 25 31.7 0.1301 0.1346 0.1230<br> <br> Back Off! I just backed up step156619.pdb to ./#step156619.pdb.1#<br> Wrote pdb files with previous and current coordinates<br> 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<br> This usually means your system is exploding,<br> if not, you should increase table-extension in your mdp file<br> <br> Step 156621, time 391.552 (ps) LINCS WARNING<br> relative constraint deviation after LINCS:<br> max 12.247591 (between atoms 9 and 16) rms 1.513366<br> bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 1 2 39.2 0.1386 0.1675 0.1390<br> 1 6 113.5 0.1403 0.0654 0.1390<br> 4 5 33.6
0.1382 0.1725 0.1390<br> 5 6 96.3 0.1412 0.0713 0.1390<br> 7 8 114.2 0.1624 0.2766 0.1530<br> 7 9 153.7 0.4814 0.9763 0.1470<br> 9 10 138.1 1.1977 0.8364 0.1470<br> 9 16 109.0 0.4632 1.7619 0.1330<br> 10 11 131.9 0.9361
0.5693 0.1530<br> 11 12 80.0 0.1536 0.6929 0.1230<br> 11 13 86.6 0.1523 0.6955 0.1330<br> 13 14 94.6 0.1088 0.3135 0.1000<br> 13 15 63.0 0.1164 0.1204 0.1000<br> 16 17 89.0 0.8288 0.5757 0.1230<br> 16 18 151.6 0.1646 0.5035 0.1530<br>
18 19 134.6 0.1550 0.2206 0.1470<br> 19 20 106.4 0.1745 0.4050 0.1470<br> 19 24 108.6 0.1639 0.4129 0.1330<br> 20 21 33.2 0.1613 0.1457 0.1530<br> 20 22 55.4 0.1634 0.1288 0.1530<br> 22 23 30.6 0.1552 0.1755 0.1530<br> 24
25 65.8 0.1345 0.1296 0.1230<br> <br> Back Off! I just backed up step156620.pdb to ./#step156620.pdb.1#<br> Wrote pdb files with previous and current coordinates<br> <br> Step 156622, time 391.555 (ps) LINCS WARNING<br> relative constraint deviation after LINCS:<br> max 156.416000 (between atoms 27 and 28) rms 43.887146<br> bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 1 2 155.9 0.1679 1.3713 0.1390<br> 1 6 165.9 0.0656 5.7379 0.1390<br> 2 3 89.1 0.1437
0.4223 0.1390<br> 3 4 89.4 0.1416 0.3068 0.1390<br> 4 5 139.8 0.1730 1.2976 0.1390<br> 5 6 169.0 0.0715 5.8196 0.1390<br> 6 7 163.1 0.5102 13.7829 0.1530<br> 7 8 147.6 0.2774 10.9817 0.1530<br> 7 9 160.5 0.9791
16.5650 0.1470<br> 9 10 170.4 0.8388 12.9173 0.1470<br> 9 16 157.1 1.7670 18.6046 0.1330<br> 10 11 160.5 0.5710 9.0364 0.1530<br> 11 12 170.7 0.6950 4.6000 0.1230<br> 11 13 170.8 0.6975 4.7046 0.1330<br> 13 14 77.3 0.3144 1.5544 0.1000<br>
13 15 51.3 0.1208 1.6563 0.1000<br> 16 17 110.0 0.5774 15.5720 0.1230<br> 16 18 118.9 0.5049 15.9163 0.1530<br> 18 19 55.9 0.2213 17.6087 0.1470<br> 19 20 56.9 0.4062 22.6568 0.1470<br> 22 23 132.0 0.1760 1.8040 0.1530<br> 24 26
44.3 0.1084 18.9838 0.1530<br> 26 27 115.3 0.1651 16.6028 0.1470<br> 27 28 78.8 0.1540 23.1402 0.1470<br> 27 36 81.3 0.1423 20.7586 0.1330<br> 28 29 109.2 0.1587 7.2465 0.1530<br> 29 30 103.3 0.1536 3.7558 0.1530<br> 30 31 50.5 0.1524 1.3613
0.1530<br> 31 32 110.6 0.1476 0.1332 0.1470<br> 32 33 65.6 0.1002 0.3047 0.1000<br> 32 34 72.2 0.1003 0.3269 0.1000<br> 32 35 66.0 0.1002 0.3122 0.1000<br> 36 37 91.3 0.1264 8.1830 0.1230<br> 36 38 90.4 0.1562 7.6206 0.1530<br>
38 39 85.9 0.1482 6.8321 0.1470<br> 39 40 72.5 0.1476 0.8344 0.1470<br> 39 48 69.1 0.1337 0.9899 0.1330<br> 40 41 79.8 0.1535 0.4217 0.1530<br> 40 42 79.3 0.1535 0.4262 0.1530<br> 42 43 42.2 0.1394 0.1974 0.1390<br> 42 47
42.6 0.1394 0.1979 0.1390<br> 48 49 68.0 0.1234 0.3369 0.1230<br> 48 50 71.2 0.1535 0.4167 0.1530<br> 50 51 58.0 0.1475 0.2531 0.1470<br> <br> Back Off! I just backed up step156621.pdb to ./#step156621.pdb.1#<br> Wrote pdb files with previous and current coordinates<br> <br> Step 156623 Warning: pressure scaling more than 1%, mu: 3.98712 3.98712 3.98712<br> Step 156623, time 391.557 (ps) LINCS WARNING<br> relative constraint deviation after LINCS:<br> max 3.089954 (between atoms 98 and 100) rms nan<br> bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br> 61 62 34.3 0.1539 0.1918 0.1530<br> 70 71 58.7 0.1479 0.2698 0.1470<br> 96 97 36.3 0.1006 0.0909 0.1000<br> 96 98 88.0 0.1338 0.3737 0.1330<br> 98 99 88.8 0.1539 0.3097 0.1530<br> 98 100 89.2 0.1237
0.5031 0.1230<br> <br> Back Off! I just backed up step156622.pdb to ./#step156622.pdb.1#<br> Wrote pdb files with previous and current coordinates<br> -------------------------------------------------------<br> Program mdrun, VERSION 3.3.1<br> Source code file: nsgrid.c, line: 220<br> <br> Fatal error:<br> Number of grid cells is zero. Probably the system and box collapsed.<br> <br> -------------------------------------------------------<br> <br> "I'm Gonna Get Medieval On Your Ass" (Pulp Fiction)<br> <br> <br> What is wrong and what should be done.<br> <br> redgards<br> nur<br> <p> 
        
        
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