<div class="MsoPlainText" style="MARGIN: 0in 0in 0pt"><font size="2"><font face="Courier New">Hi Group,<br>I've tried simulating a five bp dna. It has showed many atoms missing and some extra atoms present in the pdb file. For pdb2gmx, I used -ignh and -mising options. Later editconf_d, genbox_d, and genion_d steps went well. Even grompp_d worked well. But when I issued the run command for mdrun_d, the strange result is coming, repeatedly. I have installed lam-mpi and running gromacs in double precision. The commands I have used are..<br>
<br>pdb2gmx_d -f fivedna.pdb -o dna.gro -p dna.top <br>editconf_d -f dna.gro -bt dodecahedron -c -d 1.0 -o boxdna.gro<br>genbox_d -cp boxdna.gro -cs spc216.gro -p dna.top -o solvateddna.gro<br><br>neutralized the system with genion_d and grompp_d, mdrun_d with -v and -deffnm commands. Surprisigly, everytime, it is using only two cores of my core2quad processor, delaying the output for all experiments. For this experiment, here is the error report which I donot understand at all!<br>
<br>The error report is really frightening to me!!! Here it is!<br><br>[Bhanu@localhost doublestrand]$ gedit Testfile<br>[Bhanu@localhost doublestrand]$ mpirun N C Testfile<br>NNODES=2, MYRANK=1, HOSTNAME=localhost.localdomain<br>
NNODES=2, MYRANK=0, HOSTNAME=localhost.localdomain<br>NODEID=1 argc=6<br>NODEID=0 argc=6<br><span style="mso-spacerun: yes"> </span>:-)<span style="mso-spacerun: yes"> </span>G<span style="mso-spacerun: yes"> </span>R<span style="mso-spacerun: yes"> </span>O<span style="mso-spacerun: yes"> </span>M<span style="mso-spacerun: yes"> </span>A <span style="mso-spacerun: yes"> </span>C<span style="mso-spacerun: yes"> </span>S<span style="mso-spacerun: yes"> </span>(-:<br>
<br><span style="mso-spacerun: yes"> </span>GRowing Old MAkes el Chrono Sweat<br><br><span style="mso-spacerun: yes"> </span>:-)<span style="mso-spacerun: yes"> </span>VERSION 4.0.3<span style="mso-spacerun: yes"> </span>(-:<br>
<br><br><span style="mso-spacerun: yes"> </span>Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br><span style="mso-spacerun: yes"> </span>Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br>
<span style="mso-spacerun: yes"> </span>Copyright (c) 2001-2008, The GROMACS development team,<br><span style="mso-spacerun: yes"> </span>check out <a href="http://www.gromacs.org">http://www.gromacs.org</a> for more information.<br>
<br><span style="mso-spacerun: yes"> </span>This program is free software; you can redistribute it and/or<br><span style="mso-spacerun: yes"> </span>modify it under the terms of the GNU General Public License<br>
<span style="mso-spacerun: yes"> </span>as published by the Free Software Foundation; either version 2<br><span style="mso-spacerun: yes"> </span>of the License, or (at your option) any later version.<br>
<br><span style="mso-spacerun: yes"> </span>:-)<span style="mso-spacerun: yes"> </span>mdrun_d (double precision)<span style="mso-spacerun: yes"> </span>(-:<br><br>Option<span style="mso-spacerun: yes"> </span>Filename<span style="mso-spacerun: yes"> </span>Type<span style="mso-spacerun: yes"> </span>Description<br>
------------------------------------------------------------<br><span style="mso-spacerun: yes"> </span>-s<span style="mso-spacerun: yes"> </span>bhanu.tpr<span style="mso-spacerun: yes"> </span>Input<span style="mso-spacerun: yes"> </span>Run input file: tpr tpb tpa<br>
<span style="mso-spacerun: yes"> </span>-o<span style="mso-spacerun: yes"> </span>bhanu.trr<span style="mso-spacerun: yes"> </span>Output<span style="mso-spacerun: yes"> </span>Full precision trajectory: trr trj cpt<br>
<span style="mso-spacerun: yes"> </span>-x<span style="mso-spacerun: yes"> </span>bhanu.xtc<span style="mso-spacerun: yes"> </span>Output, Opt. Compressed trajectory (portable xdr format)<br>-cpi<span style="mso-spacerun: yes"> </span>bhanu.cpt<span style="mso-spacerun: yes"> </span>Input, Opt.<span style="mso-spacerun: yes"> </span>Checkpoint file<br>
-cpo<span style="mso-spacerun: yes"> </span>bhanu.cpt<span style="mso-spacerun: yes"> </span>Output, Opt. Checkpoint file<br><span style="mso-spacerun: yes"> </span>-c<span style="mso-spacerun: yes"> </span>bhanu.gro<span style="mso-spacerun: yes"> </span>Output<span style="mso-spacerun: yes"> </span>Structure file: gro g96 pdb<br>
<span style="mso-spacerun: yes"> </span>-e<span style="mso-spacerun: yes"> </span>bhanu.edr<span style="mso-spacerun: yes"> </span>Output<span style="mso-spacerun: yes"> </span>Energy file: edr ene<br><span style="mso-spacerun: yes"> </span>-g<span style="mso-spacerun: yes"> </span>bhanu.log<span style="mso-spacerun: yes"> </span>Output<span style="mso-spacerun: yes"> </span>Log file<br>
-dgdl<span style="mso-spacerun: yes"> </span>bhanu.xvg<span style="mso-spacerun: yes"> </span>Output, Opt. xvgr/xmgr file<br>-field<span style="mso-spacerun: yes"> </span>bhanu.xvg<span style="mso-spacerun: yes"> </span>Output, Opt. xvgr/xmgr file<br>
-table<span style="mso-spacerun: yes"> </span>bhanu.xvg<span style="mso-spacerun: yes"> </span>Input, Opt.<span style="mso-spacerun: yes"> </span>xvgr/xmgr file<br>-tablep<span style="mso-spacerun: yes"> </span>bhanu.xvg<span style="mso-spacerun: yes"> </span>Input, Opt.<span style="mso-spacerun: yes"> </span>xvgr/xmgr file<br>
-tableb<span style="mso-spacerun: yes"> </span><span style="mso-spacerun: yes"> </span>bhanu.xvg<span style="mso-spacerun: yes"> </span>Input, Opt.<span style="mso-spacerun: yes"> </span>xvgr/xmgr file<br>-rerun<span style="mso-spacerun: yes"> </span>bhanu.xtc<span style="mso-spacerun: yes"> </span>Input, Opt.<span style="mso-spacerun: yes"> </span>Trajectory: xtc trr trj gro g96 pdb cpt<br>
-tpi<span style="mso-spacerun: yes"> </span>bhanu.xvg<span style="mso-spacerun: yes"> </span>Output, Opt. xvgr/xmgr file<br>-tpid<span style="mso-spacerun: yes"> </span>bhanu.xvg<span style="mso-spacerun: yes"> </span>Output, Opt. xvgr/xmgr file<br>
<span style="mso-spacerun: yes"> </span>-ei<span style="mso-spacerun: yes"> </span>bhanu.edi<span style="mso-spacerun: yes"> </span>Input, Opt.<span style="mso-spacerun: yes"> </span>ED sampling input<br><span style="mso-spacerun: yes"> </span>-eo<span style="mso-spacerun: yes"> </span>bhanu.edo<span style="mso-spacerun: yes"> </span>Output, Opt. ED sampling output<br>
<span style="mso-spacerun: yes"> </span>-j<span style="mso-spacerun: yes"> </span>bhanu.gct<span style="mso-spacerun: yes"> </span>Input, Opt.<span style="mso-spacerun: yes"> </span>General coupling stuff<br><span style="mso-spacerun: yes"> </span>-jo<span style="mso-spacerun: yes"> </span>bhanu.gct<span style="mso-spacerun: yes"> </span>Output, Opt. General coupling stuff<br>
-ffout<span style="mso-spacerun: yes"> </span>bhanu.xvg<span style="mso-spacerun: yes"> </span>Output, Opt. xvgr/xmgr file<br>-devout<span style="mso-spacerun: yes"> </span>bhanu.xvg<span style="mso-spacerun: yes"> </span>Output, Opt. xvgr/xmgr file<br>
-runav<span style="mso-spacerun: yes"> </span>bhanu.xvg<span style="mso-spacerun: yes"> </span>Output, Opt. xvgr/xmgr file<br><span style="mso-spacerun: yes"> </span>-px<span style="mso-spacerun: yes"> </span>bhanu.xvg<span style="mso-spacerun: yes"> </span>Output, Opt. xvgr/xmgr file<br>
<span style="mso-spacerun: yes"> </span>-pf<span style="mso-spacerun: yes"> </span>bhanu.xvg<span style="mso-spacerun: yes"> </span>Output, Opt. xvgr/xmgr file<br>-mtx<span style="mso-spacerun: yes"> </span>bhanu.mtx<span style="mso-spacerun: yes"> </span>Output, Opt. Hessian matrix<br>
<span style="mso-spacerun: yes"> </span>-dn<span style="mso-spacerun: yes"> </span>bhanu.ndx<span style="mso-spacerun: yes"> </span>Output, Opt. Index file<br><br>Option<span style="mso-spacerun: yes"> </span>Type<span style="mso-spacerun: yes"> </span>Value<span style="mso-spacerun: yes"> </span>Description<br>
------------------------------------------------------<br>-[no]h<span style="mso-spacerun: yes"> </span>bool<span style="mso-spacerun: yes"> </span>no<span style="mso-spacerun: yes"> </span>Print help info and quit<br>
-nice<span style="mso-spacerun: yes"> </span>int<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>Set the nicelevel<br>-deffnm<span style="mso-spacerun: yes"> </span>string bhanu<span style="mso-spacerun: yes"> </span>Set the default filename for all file options<br>
-[no]xvgr<span style="mso-spacerun: yes"> </span>bool<span style="mso-spacerun: yes"> </span>yes<span style="mso-spacerun: yes"> </span>Add specific codes (legends etc.) in the output<br><span style="mso-spacerun: yes"> </span>xvg files for the xmgrace program<br>
-[no]pd<span style="mso-spacerun: yes"> </span>bool<span style="mso-spacerun: yes"> </span>no<span style="mso-spacerun: yes"> </span>Use particle decompostion<br>-dd<span style="mso-spacerun: yes"> </span>vector 0 0 0<span style="mso-spacerun: yes"> </span>Domain decomposition grid, 0 is optimize<br>
-npme<span style="mso-spacerun: yes"> </span>int<span style="mso-spacerun: yes"> </span>-1<span style="mso-spacerun: yes"> </span>Number of separate nodes to be used for PME, -1<br><span style="mso-spacerun: yes"> </span>is guess<br>
-ddorder<span style="mso-spacerun: yes"> </span>enum<span style="mso-spacerun: yes"> </span>interleave<span style="mso-spacerun: yes"> </span>DD node order: interleave, pp_pme or cartesian<br>-[no]ddcheck bool<span style="mso-spacerun: yes"> </span>yes<span style="mso-spacerun: yes"> </span>Check for all bonded interactions with DD<br>
-rdd<span style="mso-spacerun: yes"> </span>real<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>The maximum distance for bonded interactions with<br><span style="mso-spacerun: yes"> </span>DD (nm), 0 is determine from initial coordinates<br>
-rcon<span style="mso-spacerun: yes"> </span>real<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>Maximum distance for P-LINCS (nm), 0 is estimate<br>-dlb<span style="mso-spacerun: yes"> </span>enum<span style="mso-spacerun: yes"> </span>auto<span style="mso-spacerun: yes"> </span>Dynamic load balancing (with DD): auto, no or yes<br>
-dds<span style="mso-spacerun: yes"> </span>real<span style="mso-spacerun: yes"> </span>0.8<span style="mso-spacerun: yes"> </span>Minimum allowed dlb scaling of the DD cell size<br>-[no]sum<span style="mso-spacerun: yes"> </span>bool<span style="mso-spacerun: yes"> </span>yes<span style="mso-spacerun: yes"> </span>Sum the energies at every step<br>
-[no]v<span style="mso-spacerun: yes"> </span>bool<span style="mso-spacerun: yes"> </span>yes<span style="mso-spacerun: yes"> </span>Be loud and noisy<br>-[no]compact bool<span style="mso-spacerun: yes"> </span>yes<span style="mso-spacerun: yes"> </span>Write a compact log file<br>
-[no]seppot<span style="mso-spacerun: yes"> </span>bool<span style="mso-spacerun: yes"> </span>no<span style="mso-spacerun: yes"> </span>Write separate V and dVdl terms for each<br><span style="mso-spacerun: yes"> </span>interaction type and node to the log file(s)<br>
-pforce<span style="mso-spacerun: yes"> </span>real<span style="mso-spacerun: yes"> </span>-1<span style="mso-spacerun: yes"> </span>Print all forces larger than this (kJ/mol nm)<br>-[no]reprod<span style="mso-spacerun: yes"> </span>bool<span style="mso-spacerun: yes"> </span>no<span style="mso-spacerun: yes"> </span>Try to avoid optimizations that affect binary<br>
<span style="mso-spacerun: yes"> </span>reproducibility<br>-cpt<span style="mso-spacerun: yes"> </span>real<span style="mso-spacerun: yes"> </span>15<span style="mso-spacerun: yes"> </span>Checkpoint interval (minutes)<br>
-[no]append<span style="mso-spacerun: yes"> </span>bool<span style="mso-spacerun: yes"> </span>no<span style="mso-spacerun: yes"> </span>Append to previous output files when restarting<br><span style="mso-spacerun: yes"> </span>from checkpoint<br>
-maxh<span style="mso-spacerun: yes"> </span>real<span style="mso-spacerun: yes"> </span>-1<span style="mso-spacerun: yes"> </span>Terminate after 0.99 times this time (hours)<br>-multi<span style="mso-spacerun: yes"> </span>int<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>Do multiple simulations in parallel<br>
-replex<span style="mso-spacerun: yes"> </span>int<span style="mso-spacerun: yes"> </span>0<span style="mso-spacerun: yes"> </span>Attempt replica exchange every # steps<br>-reseed<span style="mso-spacerun: yes"> </span>int<span style="mso-spacerun: yes"> </span>-1<span style="mso-spacerun: yes"> </span>Seed for replica exchange, -1 is generate a seed<br>
-[no]glas<span style="mso-spacerun: yes"> </span>bool<span style="mso-spacerun: yes"> </span>no<span style="mso-spacerun: yes"> </span>Do glass simulation with special long range<br><span style="mso-spacerun: yes"> </span>corrections<br>
-[no]ionize<span style="mso-spacerun: yes"> </span>bool<span style="mso-spacerun: yes"> </span>no<span style="mso-spacerun: yes"> </span>Do a simulation including the effect of an X-Ray<br><span style="mso-spacerun: yes"> </span>bombardment on your system<br>
<br>Getting Loaded...<br>Reading file bhanu.tpr, VERSION 4.0.3 (double precision)<br>Loaded with Money<br><br>Making 1D domain decomposition 2 x 1 x 1<br>Steepest Descents:<br><span style="mso-spacerun: yes"> </span>Tolerance (Fmax)<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>1.00000e+01<br>
<span style="mso-spacerun: yes"> </span>Number of steps<span style="mso-spacerun: yes"> </span>=<span style="mso-spacerun: yes"> </span>10000<br>Step=<span style="mso-spacerun: yes"> </span>0, Dmax= 1.0e-02 nm, Epot=<span style="mso-spacerun: yes"> </span>nan Fmax= 5.33517e+22, atom= 99<br>
-------------------------------------------------------<br>Program mdrun_d, VERSION 4.0.3<br>Source code file: nsgrid.c, line: 357<br><br>Range checking error:<br>Explanation: During neighborsearching, we assign each particle to a grid<br>
based on its coordinates. If your system contains collisions or parameter<br>errors that give particles very high velocities you might end up with some<br>coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot<br>
put these on a grid, so this is usually where we detect those errors.<br>Make sure your system is properly energy-minimized and that the potential<br>energy seems reasonable before trying again.<br><br>Variable ci has value -2147483607. It should have been within [ 0 .. 280 ]<br>
<br>-------------------------------------------------------<br><br>"One Ripple At a Time" (Bianca's Smut Shack)<br><br>Error on node 0, will try to stop all the nodes<br>Halting parallel program mdrun_d on CPU 0 out of 2<br>
<br>-------------------------------------------------------<br>Program mdrun_d, VERSION 4.0.3<br>Source code file: nsgrid.c, line: 357<br><br>Range checking error:<br>Explanation: During neighborsearching, we assign each particle to a grid<br>
based on its coordinates. If your system contains collisions or parameter<br>errors that give particles very high velocities you might end up with some<br>coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot<br>
put these on a grid, so this is usually where we detect those errors.<br>Make sure your system is properly energy-minimized and that the potential<br>energy seems reasonable before trying again.<br><br>Variable ci has value -2147483607. It should have been within [ 0 .. 280 ]<br>
<br>-------------------------------------------------------<br><br>"One Ripple At a Time" (Bianca's Smut Shack)<br><br>Error on node 1, will try to stop all the nodes<br>Halting parallel program mdrun_d on CPU 1 out of 2<br>
<br>gcq#142: "One Ripple At a Time" (Bianca's Smut Shack)<br><br>-----------------------------------------------------------------------------<br>One of the processes started by mpirun has exited with a nonzero exit<br>
code.<span style="mso-spacerun: yes"> </span>This typically indicates that the process finished in error.<br>If your process did not finish in error, be sure to include a "return<br>0" or "exit(0)" in your C code before exiting the application.<br>
<br>PID 18729 failed on node n0 (127.0.0.1) with exit status 1.<br>-----------------------------------------------------------------------------</font></font></div>
<p><font size="2"><font face="Courier New"></font></font> </p>
<div><font size="2"><font face="Courier New"></font></font> </div>
<div><font size="2"><font face="Courier New"></font></font> </div>
<div><font size="2"><font face="Courier New"></font></font> </div>
<div><font size="2"><font face="Courier New"></font></font> </div>
<div><font size="2"><font face="Courier New"></font></font> </div>
<div><font size="2"><font face="Courier New">I tried changing the ns-type to simple, from Grid.. no success yet! Any suggestions friends???</font></font></div>
<div><font size="2"><font face="Courier New"></font></font> </div>
<div><font size="2"><font face="Courier New"></font></font> </div>
<div><font size="2"><font face="Courier New">Bhanu Prakash.</font></font></div>
<div class="MsoPlainText" style="MARGIN: 0in 0in 0pt"><br> </div><br clear="all"><br>