<div style="text-align: left;"><font class="Apple-style-span" face="arial, helvetica, sans-serif">Hello,</font></div><div><div style="text-align: left;"><font class="Apple-style-span" face="arial, helvetica, sans-serif"><br>
</font></div><div style="text-align: left;"><font class="Apple-style-span" face="arial, helvetica, sans-serif">The last 6 months I've been working with gromacs (4.5.3 and 4.5.4) in Ubuntu (10.4) and it has worked fine. The problem started when I changed the linux distribution to Scientific Linux (5.3)... I followed the same steps to download/configure gromacs but something's wrong or missing because the simulations that I had been running on UBUNTU crashed in SL. </font></div>
<div style="text-align: left;"><font class="Apple-style-span" face="arial, helvetica, sans-serif"><br></font></div><div style="text-align: left;"><font class="Apple-style-span" face="arial, helvetica, sans-serif">The command I use is very simple:</font></div>
<div style="text-align: left;"><font class="Apple-style-span" face="arial, helvetica, sans-serif"><br></font></div><div style="text-align: left;"><i><font class="Apple-style-span" face="arial, helvetica, sans-serif"> mdrun -v -s topol.tpr</font></i></div>
<div style="text-align: left;"><font class="Apple-style-span" face="arial, helvetica, sans-serif"><br></font></div><div style="text-align: left;"><font class="Apple-style-span" face="arial, helvetica, sans-serif">In Ubuntu the simulation ends fine but in SL</font><span class="Apple-style-span" style="font-family: arial, helvetica, sans-serif; "> the application starts to write on prompt a</span>t early steps (around 100)</div>
<div style="text-align: left;"><font class="Apple-style-span" face="arial, helvetica, sans-serif"><br></font></div><div><div style="text-align: left;"><i><font class="Apple-style-span" face="arial, helvetica, sans-serif">Step XX, time 0.XX (ps) LINCS WARNING</font></i></div>
<div style="text-align: left;"><i><font class="Apple-style-span" face="arial, helvetica, sans-serif">relative constraint deviation after LINCS:</font></i></div><div style="text-align: left;"><i><font class="Apple-style-span" face="arial, helvetica, sans-serif">rms XX, max XX (between atoms XX and XX)</font></i></div>
<div style="text-align: left;"><i><font class="Apple-style-span" face="arial, helvetica, sans-serif">bonds that rotated more than 30 degrees:</font></i></div></div><div><div style="text-align: left;"><i><font class="Apple-style-span" face="arial, helvetica, sans-serif">...</font></i></div>
<i><span class="Apple-style-span" style="font-style: normal; "><i><font class="Apple-style-span" face="arial, helvetica, sans-serif">Wrote pdb files with previous and current coordinates</font></i></span></i></div><div style="text-align: left;">
<i><font class="Apple-style-span" face="arial, helvetica, sans-serif"><br></font></i></div><div style="text-align: left;"><font class="Apple-style-span" face="arial, helvetica, sans-serif">Until the simulation ends (around 250) with a message of</font></div>
<div style="text-align: left;"><font class="Apple-style-span" face="arial, helvetica, sans-serif"><br></font></div><div><i><div style="text-align: left;"><font class="Apple-style-span" face="arial, helvetica, sans-serif">Segmentation fault</font></div>
</i></div><div style="text-align: left;"><font class="Apple-style-span" face="arial, helvetica, sans-serif"><br></font></div><div style="text-align: left;"><font class="Apple-style-span" face="arial, helvetica, sans-serif"><br>
</font></div><div style="text-align: left;"><font class="Apple-style-span" face="arial, helvetica, sans-serif">I tried different ways to configure gromacs but none of them seems to resolve the problem</font></div><div style="text-align: left;">
<font class="Apple-style-span" face="arial, helvetica, sans-serif">1) ./configure --prefix=<my path></font></div><div style="text-align: left;"><font class="Apple-style-span" face="arial, helvetica, sans-serif">make</font></div>
<div style="text-align: left;"><font class="Apple-style-span" face="arial, helvetica, sans-serif">make install</font></div><div style="text-align: left;"><font class="Apple-style-span" face="arial, helvetica, sans-serif"><br>
</font></div><div style="text-align: left;"><font class="Apple-style-span" face="arial, helvetica, sans-serif">2) ./configure --with-fft=fftw3 --prefix=<my path> --without-x</font></div><div><div style="text-align: left;">
<div style="text-align: left; "><font class="Apple-style-span" face="arial, helvetica, sans-serif">make</font></div><div style="text-align: left; "><font class="Apple-style-span" face="arial, helvetica, sans-serif">make install</font></div>
<div style="text-align: left; "><font class="Apple-style-span" face="arial, helvetica, sans-serif"><br></font></div><div style="text-align: left; "><font class="Apple-style-span" face="arial, helvetica, sans-serif">3)./configure --program-suffix= --disable-float --prefix=<my path> --exec-prefix=<my path> --enable-all-static --with-fft=fftw3 --without-x</font></div>
<div style="text-align: left; "><font class="Apple-style-span" face="arial, helvetica, sans-serif"><div style="font-family: arial; text-align: left; "><font class="Apple-style-span" face="arial, helvetica, sans-serif">make</font></div>
<div style="font-family: arial; text-align: left; "><font class="Apple-style-span" face="arial, helvetica, sans-serif">make install</font></div><div style="font-family: arial; text-align: left; "><font class="Apple-style-span" face="arial, helvetica, sans-serif"><br>
</font></div><div style="text-align: left; ">Moreover, I downloaded the benchmark posted in the gromacs web page to test the simulations with other ".tpr" files. I run the first simulation (implicit solvent) in UBUNTU and worked OK but the one on SL crashed (around step 460) with the first two options of configuration. The last configuration enabled the simulation to run OK( I decided to stop it at 4000 steps)...</div>
<div style="text-align: left; ">This bewilders me because the last configuration permitted the benchmark to run OK but not my file. I don't think my file has an unstable system because it works all right in UBUNTU (and also Debian!)</div>
<div style="font-family: arial; text-align: left; "><font class="Apple-style-span" face="arial, helvetica, sans-serif"><br></font></div><br></font><font class="Apple-style-span" face="arial, helvetica, sans-serif"><span class="Apple-style-span" style="font-family: arial; "><div style="text-align: left; ">
<font class="Apple-style-span" face="arial, helvetica, sans-serif">In addition, I </font>upgraded my linux distribution to the latest SL 5.x release but it didn't make any change!</div><div style="text-align: left; ">
<br></div><div style="text-align: left; "><br></div><div style="text-align: left; ">I hope you can help me with some guide on how to proceed a GOOD instalation in SL or to let me know what is my problem and what I am missing. </div>
<div style="text-align: left; "> </div><div style="text-align: left; "><br></div></span></font></div></div><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; background-color: rgb(255, 255, 255); ">Thank you for four answer,</span><font class="Apple-style-span" face="arial, helvetica, sans-serif"><span class="Apple-style-span" style="background-color: rgb(255, 255, 255); "><span class="Apple-style-span" style="white-space: pre;"><br>
</span></span><br></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif">Nathalia Garces</font></div><div></div></div>