<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div style="font-family: lucida console,sans-serif;">
<meta http-equiv="CONTENT-TYPE" content="text/html; charset=utf-8"><title></title>
<meta name="GENERATOR" content="BrOffice.org 3.1 (Unix)">
<style type="text/css">
<!--
@page { margin: 2cm }
P { margin-bottom: 0.21cm }
-->
</style>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">Dear
Gromacs users;</span></font></p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;" lang="en-US">
<br>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">I
have got a problem when performing </span></font><font size="2"><span lang="en-US">molecular
dynamics calculations in double precision with Gromacs Version 4.0.7.
My system contains a protein with 482 residues, water molecules and
Cl-ions. </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">I
have already carried out this same calculation in single precision
with success.</span></font></p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">Below,
I show my output and input files for the calculation in double
precision.</span></font></p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US"><<<<===============================================================>>>></span></font></p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">starting
mdrun 'Protein in water' </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">1000000
steps, 2000.0 ps. </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">Warning:
1-4 interaction between 4412 and 4417 at distance inf which is larger
than the 1-4 table size 2.400 nm </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">These
are ignored for the rest of the simulation </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">This
usually means your system is exploding, </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">if
not, you should increase table-extension in your mdp file </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">or
with user tables increase the table size </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">Warning:
1-4 interaction between 4365 and 4368 at distance inf which is larger
than the 1-4 table size 2.400 nm </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">These
are ignored for the rest of the simulation </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">This
usually means your system is exploding, </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">if
not, you should increase table-extension in your mdp file </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">or
with user tables increase the table size </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">Warning:
1-4 interaction between 4649 and 4655 at distance inf which is larger
than the 1-4 table size 2.400 nm </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">These
are ignored for the rest of the simulation </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">Warning:
1-4 interaction between 1336 and 1339 at distance inf which is larger
than the 1-4 table size 2.400 nm </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">This
usually means your system is exploding, </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">if
not, you should increase table-extension in your mdp file </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">or
with user tables increase the table size </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">These
are ignored for the rest of the simulation </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">This
usually means your system is exploding, </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">if
not, you should increase table-extension in your mdp file </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">or
with user tables increase the table size </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">Warning:
1-4 interaction between 1199 and 1211 at distance inf which is larger
than the 1-4 table size 2.400 nm </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">These
are ignored for the rest of the simulation </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">This
usually means your system is exploding, </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">if
not, you should increase table-extension in your mdp file </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">or
with user tables increase the table size </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">Warning:
1-4 interaction between 525 and 529 at distance inf which is larger
than the 1-4 table size 2.400 nm </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">These
are ignored for the rest of the simulation </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">This
usually means your system is exploding, </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">if
not, you should increase table-extension in your mdp file </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">or
with user tables increase the table size </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">rank
2 in job 7 slayer_37486 caused collective abort of all ranks </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">exit
status of rank 2: killed by signal 9</span></font></p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US"><<<<===============================================================>>>></span></font></p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;" lang="en-US">
<br>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">My
mdp file is:</span></font></p>
<p class="western" style="margin-bottom: 0cm; line-height: 100%;" lang="en-US">
<br>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US"><<<<<==============================================================>>>></span></font></p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">title
: ldtop1 </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">cpp :
/usr/bin/cpp ; the c processor </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">integrator
: md </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">dt :
0.002 </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">nsteps:
1000000 </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">nstcomm:1
</span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">nstxout:500
</span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">nstvout:500
</span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">nstfout:0
</span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">nstlist:5
</span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">ns_type:grid
</span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">rlist:0.9
</span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">coulombtype:PME
</span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">rcoulomb:0.9
</span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">rvdw:1.4
</span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">table-extension:4.000
</span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">fourierspacing:0.12
</span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">fourier_nx:0
</span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">fourier_ny:0
</span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">fourier_nz:0
</span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">pme_order:14
</span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">ewald_rtol:1e-5
</span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">optimize_fft:yes
</span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">constraint_algorithm:LINCS
</span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">constraints:hbonds
</span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">lincs_order
:6 </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">; </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">;
Berendsen temperature coupling </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">; </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">Tcoupl
: V-rescale </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">tau_t
: 0.1 0.1 0.1 </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">tc-grps:
protein SOL CL- </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">ref_t
: 300 300 300 </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">;</span></font></p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">;
Pressure Coupling </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">;</span></font></p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">Pcoupl
: berendsen </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">pcoupltype:
isotropic </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">tau_p
: 0.5 </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">compressibility
: 4.5e-5 </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">ref_p
: 1.0 </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">;</span></font></p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">;
Generate velocity </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">;</span></font></p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">gen_vel:
yes </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">gen_temp
: 300.0 </span></font>
</p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">gen_seed
: 173529</span></font></p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US"><<<<===============================================================>>>></span></font></p>
<p class="western" style="margin-top: 0.05cm; margin-bottom: 0cm; line-height: 100%;">
<font size="2"><span lang="en-US">Any
help would be appreciated, and if you require further information
please let me know.</span></font></p>
<p class="western" style="margin-bottom: 0cm;"><font size="2"><span lang="en-US"><br></span></font><font size="2">Thanks
in advance.</font></p>
<p class="western" style="margin-bottom: 0cm;"><font size="2">Jesse
da Nóbrega</font></p>
</div>
<!-- cg2.c903.mail.sp2.yahoo.com compressed/chunked Fri Dec 11 16:30:19 PST 2009 -->
</div><br>
<hr size=1>Veja quais são os assuntos do momento no Yahoo! + Buscados: <a href="http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/">Top 10</a> - <a href="http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/celebridades/">Celebridades</a> - <a href="http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/m%C3%BAsica/">Música</a> - <a href="http://br.rd.yahoo.com/mail/taglines/mail/*http://br.maisbuscados.yahoo.com/esportes/">Esportes</a></body></html>