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<p class="MsoNormal">Dear all</p>
<p class="MsoNormal">I am trying to simulate a Lennard-Jones
coarse-grained
polymer melt. Until know I simulated only one chain, in order to check
if the
parameters I used are OK.</p>
<p class="MsoNormal">I simulated one chain of 50 LJ particles with <b><span lang="EL">å</span>=1KJ/mol, m=1gr/mol, <span lang="EL">ó</span>=1nm</b>.
This means that my characteristic
time of the system <b><span lang="EL">ô</span>=<span lang="EL">ó</span>(m/<span lang="EL">å</span>)<sup>1/2</sup></b> is <b><span lang="EL">ô</span>=1ps.
</b></p>
<p class="MsoNormal">I am using RIGID bonds between the particles also
with
length <b><span lang="EL">ó</span>=1nm</b>. </p>
<p class="MsoNormal">I have seen in many papers which are using similar
systems
that the time step they use is Dt=0.01<span lang="EL">ô</span>. </p>
<p class="MsoNormal">When I use <b>Dt=0.01<span lang="EL">ô</span></b> I
don’t get any error messages in my <b>.log</b> file or in the resulting
<b>.gro</b> file.</p>
<p class="MsoNormal">The problem that I have is when I am trying to
convert my
<b>.xtc</b> file to <b>.pdb</b> in order to visualize it in VMD.</p>
<p class="MsoNormal">When I use:</p>
<p class="MsoNormal"><b>trjconv –f <span> </span><i>***.xtc</i> <span> </span>-s
<i>***.tpr</i> <span> </span>-o <i>***.pdb</i> <span> </span>-pbc
<i>whole</i></b></p>
<p class="MsoNormal">the trajectory looks fine. </p>
<p class="MsoNormal">BUT, when I use </p>
<p class="MsoNormal"><b>trjconv <span> </span>–f <span></span><i>***.xtc</i><span>
</span><span> </span>-s<i> ***.tpr</i> <span> </span>-o <i>***.pdb </i><span> </span>–pbc
<i>nojump</i></b></p>
<p class="MsoNormal">, it seems the chain is blowing after few steps
(the
bonds break and the particles spread in every direction).</p>
<p class="MsoNormal">I would think that for a single chain, these two
options of
trjconv should not make such a difference.</p>
<p class="MsoNormal">I used a relatively big box for the simulation (10 X
10 X 60). The <i><b>strange</b></i> think is that I don’t have this problem
when I increase
the box size (to 50X50X60) , or of course when I decrease the time step.</p>
<p class="MsoNormal">Is it possible that I am not able to use such a
large
time-step in GROMACS, or is it something with the <b>trjconv</b> that I
don’t
understand ?</p><p class="MsoNormal">Thanks in advance<br></p>
<p class="MsoNormal">Best Regards, Chrysostomos</p>
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