After EM, I got:<br><br>Potential Energy  =  1.7242092e+05<br>Maximum force     =  2.1079963e+03 on atom 675<br>Norm of force     =  5.9417034e+01<br><br>I think my system size is too big compared to the box size so I am going to run the simulation with smaller number of molecules to see whether this helps or not.<br>
<br><br><div class="gmail_quote">On Fri, Oct 9, 2009 at 11:22 AM, Justin A. Lemkul <span dir="ltr">&lt;<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
Yongchul Chung wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
yes I carried out energy minimization and used following parameters.<br>
<br>
</blockquote>
<br></div>
OK, so what values of potential energy and maximum force did EM achieve?<br><font color="#888888">
<br>
-Justin</font><div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
title               =  FWS<br>
cpp                 =  /usr/bin/cpp ; the c pre-processor define              =  -DFLEXIBLE<br>
constraints         =  none<br>
integrator          =  steep<br>
dt                  =  0.002    ; ps !<br>
nsteps              =  1000<br>
nstlist             =  10 ns_type             =  grid<br>
rlist               =  1.0<br>
coulombtype         =  PME<br>
rcoulomb            =  1.0<br>
vdwtype             =  cut-off<br>
rvdw                =  1.4<br>
fourierspacing  =  0.12<br>
fourier_nx  =  0<br>
fourier_ny  =  0<br>
fourier_nz  =  0<br>
pme_order  =  4<br>
ewald_rtol  =  1e-5<br>
optimize_fft  =  yes<br>
;<br>
;       Energy minimizing stuff<br>
;<br>
emtol               =  500<br>
emstep              =  0.01<br>
<br>
<br>
</blockquote>
<br></div><div><div></div><div class="h5">
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Yongchul &quot;Greg&quot; Chung<br>Graduate Student<br>Dept. of Chemical Engineering, Case Western Reserve University<br>