Dear Gromacs Users:<br>
I have a question and I hope you can help me. I want to
simulate a LJ-system in reduced units to reproduce the values of
<span><span>Mol. Phys. 78, 591-618</span></span> (page 595). I made my
<span style="font-weight: bold;">grompp.mdp</span>, <span style="font-weight: bold;">conf.gro</span> and <span style="font-weight: bold;">topo1.top</span>
(Please see attached file) and I simulated the system and I got the value close to the
rigth pression, but the answer was wrong for the potential (I
got almost the potential but times 1000). I<font size="-1"> tried various other </font> values
and I got the same thing. I don't know where the error is? . What i did is:<br>
<ul>
<li><span style="font-weight: bold;"><span style="font-weight: bold;"></span><span style="color: rgb(255, 102, 102);">grompp.mdp</span></span><span style="color: rgb(255, 102, 102);">.</span>- I set up <span style="font-weight: bold;">
reduced temperature= <span style="font-weight: bold;">5</span></span>,<span style="font-weight: bold;">
rcut-off =4</span> (rvdw), and Temperature coupling = Berendsen.</li>
</ul>
<ul>
<li><span style="font-weight: bold;"><span style="font-weight: bold;"></span><span style="color: rgb(255, 102, 102);">conf.gro</span></span>.- <span style="font-weight: bold;">reduced density = 0.4</span>
(864 atoms and box size 12.92660x12.92660x12.92660) I generated the
initial positions as SC also in reduce units (simple cubic).
</li>
</ul>
<ul>
<li> <span style="font-weight: bold; color: rgb(255, 102, 102);">topo1.top</span>.- I set up <span style="font-weight: bold;">epsilon=1</span>, <span style="font-weight: bold;">sigma=1</span> and <span style="font-weight: bold;">
mass=1, </span>following the manual reference.</li>
</ul>
<font size="-1"> </font>Could
someone help me? Has <font size="-1">Anybody done any simulation in reduce units?, </font> Thanks in advance.<br>
<br>
P.S.: gromacs gives the pression in bar ===> presion [in reduced units ] = 16.6054*pression (in md.log file)<br clear="all"><br>-- <br>Cheers, <br> <br>Paul CARDENAS LIZANA<br><a href="mailto:g943189@oz.nthu.edu.tw">
g943189@oz.nthu.edu.tw</a> / <a href="mailto:paulclizana@gmail.com">paulclizana@gmail.com</a><br>National Tsing Hua University (ÇåÈA´óŒW)<br><br>ÖxÖxÄãµÄŽÍæ<br>I appreciate your help. Thanks!<br>Os agradezco la ayuda. Gracias!