[gmx-users] error after mdrun
David van der Spoel
spoel at xray.bmc.uu.se
Tue Nov 14 08:08:12 CET 2006
nur avneet wrote:
> Dear All
> 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 (-:
>
your starting structure is not minimized enough.
> 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
>
> ------------------------------------------------------------------------
> Find out what India is talking about on - Yahoo! Answers India
> <http://us.rd.yahoo.com/mail/in/yanswers/*http://in.answers.yahoo.com/>
> Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8.
> Get it NOW
> <http://us.rd.yahoo.com/mail/in/messengertagline/*http://in.messenger.yahoo.com>
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
More information about the gromacs.org_gmx-users
mailing list