I've found that in general ussage of cutt-offs beetwen 0.8-1.2 nm might provide good results.<br><br>But now I have some problems with minimization of my initial structure<br><br>Firstly, I've performed steep minimization ( emtool=1000, emstep = 0.01 ) and than CG minimization (emtool=1, emstep = 0.001) but as the result I've obtain that my struucture didnt minimize properly. <br>
Is there any different strategies for the minimization for the ANM ?<br><br>In addition I'd like to know about conditions of such normal mode simulations. Does this procedure require in the PBC ? ( I've performed all steps including energy minimization in vacuu)<br>
<br><br>James<br><br><div class="gmail_quote">2011/10/25 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div text="#000000" bgcolor="#FFFFFF"><div class="im">
On 25/10/2011 3:30 AM, James Starlight wrote:
<blockquote type="cite">I understand this but I've not been able found such
information. I dont need in the most accurately parametries for
all cutt-offs of my system but I want to gain inside into the
basic cutt- offs worked with the Normal mode analysis.<br>
</blockquote>
<br></div>
The cut-offs are particular to the force field, not the manner in
which the force field is used (EM vs MD vs whatever). There are
literature references in the GROMACS manual, and also in the
published work that you have been reading because it has objectives
similar to yours. (hint, hint) <br><div class="im">
<br>
<blockquote type="cite">
<br>
E.g I've found that PME is not worked here. </blockquote>
<br></div>
PME does work here. Last time you were apparently mis-matching
files...<div class="im"><br>
<br>
<blockquote type="cite">So I must to constrain my system with simplest
cuttoffs. Could you provide me with the simple example e.g cutt of
for interaction beetwen C-alpha atoms only etc? <br>
</blockquote>
<br></div>
You can't do that, and shouldn't even if you could.<br><font color="#888888">
<br>
Mark</font><div class="im"><br>
<br>
<blockquote type="cite"><br>
James<br>
<br>
<div class="gmail_quote"><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<div> <br>
</div>
These are particular to the force field involved, not the
software. Please consult the appropriate literature, and see
what others have used for similar work.
<div><br>
</div>
</div>
</blockquote>
</div>
</blockquote>
<br>
</div></div>
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