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On 06/29/2011 04:18 PM, Ravi Kumar Venkatraman wrote:
<blockquote
cite="mid:BANLkTim62g9L6dZfWRZRjPQjU3vZRkS20g@mail.gmail.com"
type="cite">Dear all,<br>
I have been running lyz in water. I have 20 ps
pre-equilibrated NVT and 200 ps NPT configuration of spce216
water. I am following the instruction from gromacs tutorial. This
is the link for the tutorial,<br>
<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html</a><br>
<br>
After editing the box for lyz and then I tried to solvate the box
with spce216 water. I followed the same instruction but it shows
fatal I/O error - topol.top. </blockquote>
<br>
That will usually mean you've followed the instructions
incompletely. However, we don't know what you actually did do, so we
can't help other than to suggest you go back and try afresh.<br>
<br>
<blockquote
cite="mid:BANLkTim62g9L6dZfWRZRjPQjU3vZRkS20g@mail.gmail.com"
type="cite">It was not able to find the input file topol.top. But
in this tutorial its an output command. Further it shows 6091
solvent instead of 10832 as per tutorial. Pls help me find the
problem.</blockquote>
<br>
Something must be greatly different, and unless Justin's made an
error in his tutorial and you're the first to notice, it will be
something you've done.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTim62g9L6dZfWRZRjPQjU3vZRkS20g@mail.gmail.com"
type="cite"> <br clear="all">
<br>
Thank you<br>
<br>
<div><b>With Regards,</b><b><br>
</b></div>
<div><b><br>
</b></div>
<div><b>Ravi Kumar Venkatraman,</b></div>
<div><b>c/o Prof. Siva Umapathy,</b><b><br>
</b></div>
<div><b>IPC Dept., IISc.,</b></div>
<div><b>Bangalore, INDIA.</b></div>
<div><b>Phone No: +91-9686933963</b></div>
<br>
</blockquote>
<br>
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