<div>Thanks alot I did solve visualization problem using trjconv. Is it o.k. to use Berendsen thermostat for thermal unfolding of protein. I came across literature saying Berendsen coupling does not gives accurate kinetic Energy. I am using it and I am getting my protein unfolded. Am I right. Can I use the trajectory obtained for thermodynamic analysis.</div>
<div>Thanks in advance</div>
<div>msnayeem<br><br> </div>
<div><span class="gmail_quote">On 4/3/10, <b class="gmail_sendername">Justin A. Lemkul</b> <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><span class="q"><br><br>shahid nayeem wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Dear All<br>I am working on protein unfolding<br>simulation in gromacs. when I do a production run on 32 node HPC I get<br>
.trr file along with .gro. when I try to visualize this files in<br>VMD I see erratic large movement of atoms in the trajectory. With same<br>.mdp files when I did smaller run of 2ns on single PC and viewed .trr<br>and .gro in VMD, the movemnt of atom was smooth. Why this is<br>
happening. When I used the command g_filter to produce lowpass.xtc<br></blockquote><br></span>This sounds like a consequence of periodic boundary conditions. Have you tried using trjconv to fix the PBC effects (i.e., -pbc mol, -pbc nojump, or something similar)?<span class="q"><br>
<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">with -nf 10 I got the smooth movement of atoms. Is it always essential<br>to use g_filter with .trr file of HPC multinode output. what is the<br>
difference between lowpass.xtc and highpass.xtc. For the pupose of<br></blockquote><br></span>The purpose is to smooth out high-frequency vibration to make visualization a bit easier and movie-rendering more meaningful. See g_filter -h for the difference between the two; they are explained quite thoroughly.<span class="q"><br>
<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">RMSD calculation should I use the output of g_filter i.e. lowpass.xtc<br>or the original .trr file. I am new in this field so excuse me for<br>
</blockquote><br></span>Use the original (PBC-corrected) trajectory.<br><br>-Justin<span class="q"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">some basic mistakes . Any suggestion and help will highly appreciated.<br>Thanking you in advance.<br>msnayeem<br>
<br><a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:msnayeem@gmail.com" target="_blank">msnayeem@gmail.com</a><br></blockquote><br></span>-- <br>========================================<br><br>Justin A. Lemkul<br>
Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a onclick="return top.js.OpenExtLink(window,event,this)" href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a onclick="return top.js.OpenExtLink(window,event,this)" 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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