<div>Hi Mark</div>
<div>How one should be certain that this much trajectory is long enough to get coverged ensemble.</div>
<div>Shahid</div>
<div><br><br> </div>
<div><span class="gmail_quote">On 4/27/10, <b class="gmail_sendername">Mark Abraham</b> <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</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">On 27/04/2010 8:58 PM, Justin A. Lemkul wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><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 Mark<br>Following your advice I started using three peptide in one simulation<br>box. Iwas able to add these with genconf as previously in ordered<br>
manner, generated .gro with genconf, solvated it and after energy<br>minimization I did MD run for 10ns. Everything ran well. In the end<br>when I see the trajectory I find unfolding of the original chain but<br>the two additional peptide introduced through genconf show appearance<br>
of new secondary structures. Even in these two the secondary structure<br>do not develop at the same point. Why the three equivalent peptide<br>behave differently in similar environment. How can I explain this<br>observation. why the first peptide does not show any new secondary<br>
structure. Sholud I go with higher number of molecule. Will it make<br>any difference if peptides are added in disordered manner and then<br>simulated.<br></blockquote><br>Initial orientation should likely have nothing to do with it. Perhaps<br>
this is even the proper behavior for whatever your peptide is. Is its<br>structure dynamic? Is the size of your peptides large enough to even<br>believe that they would be intrinsically stable? Many model peptides, in<br>
isolation, have very transient structures.<br><br>It could also be that your simulation parameters are poorly chosen, so<br>the force field is breaking down. If you want comments on your .mdp<br>file, please post it.<br></blockquote>
<br></span>Indeed. MD is chaotic, and there's no reason to expect all peptides of any length to show the same actual behaviour in a trajectory. They might show the same behaviour in the limit of a converged ensemble, but only if aggregation is not a factor.<br>
<span class="sg"><br>Mark</span>
<div><span class="e" id="q_1283fa0c6d8c71ab_3"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">On 4/23/10, *Mark Abraham* <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>> wrote:<br><br>On 23/04/10 13:16, shahid nayeem wrote:<br><br>Dear All<br>
I am trying to study inter peptide interaction fpr which I need<br>to put<br>more than one peptide in one simulation box. I did it with genconf<br>command but this inserts peptide in a regular ordered manner I want<br>these to be in irregular disordered insertion. Even after using<br>
genconf<br><br><br>Well that's a difficult and atypical scenario. genconf -shuffle will<br>allow you to stack the same peptide in a regular array with random<br>rotations of the whole box. Then you can solvate, equilibrate and<br>
run MD at a high temperature to give yourself a quasi-disordered<br>starting state.<br><br>, I tried to proceed furthe after solvation with spc water. The<br>energy<br>minimization (steepest descent) failed to converge even after<br>
5000 steps<br>and theirafter position restraint dynamics failed giving<br>segmentation<br>fault. Introducing more peptide after generating .gro with -ci -nmol<br>gives error showing more than one residue in insert molecule.<br>
Please help me and write commands which I should follow.<br><br><br>No, because that's an impossible task. We can't begin to guess the<br>reasons for things failing without seeing the actual output (was the<br>EM energy large and negative? what was the actual error message<br>
from -ci -nmol?).<br><br>You should be careful to start with a small test case so that you<br>can learn the workflow with a manageable problem. Can you get a<br>single peptide to equilibrate? Two stacked peptides? It is best to<br>
learn to walk before trying to run :-)<br><br>Mark<br>-- gmx-users mailing list <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><mailto:<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
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