<div>Hi,</div>
<div> </div>
<div>Actually the major purpose was to extract the C-alpha components from all-atom analysis, and then compare the result with other approaches, like the PCA analysis or the GNM you mentioned. There was some discussion on this before. I guess an easy way is still to use g_nmens to generate an ensemble and run PCA on it?
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<div> </div>
<div>I am still puzzled by an old question I have asked. For the all-atom NM analysis, which force field is better, G43a1 or G43b1 (vacuum)? If I choose the normal distribution (G43a1), maybe I should use an epsilon value of 2-4 with treatments of cut-off and rcoulomb=0?
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<div>Thank you. </div>
<div> </div>
<div>Lei Zhou<br><br> </div>
<div><span class="gmail_quote">On 5/16/06, <b class="gmail_sendername">Erik Lindahl</b> <<a href="mailto:lindahl@sbc.su.se">lindahl@sbc.su.se</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi,<br><br>On May 15, 2006, at 10:02 PM, Lei Zhou wrote:<br><br>> Hi,<br>><br>> I am trying to convert the binary Hessian matrix (
nm.mtx) into a<br>> readable ascii format. According to the recommendations on this<br>> email list, I rename the nm.mtx to nm.trr and tried to use gmxdump.<br>> However, there is an error message liketrn version:
<br>><br>> Program gmxdump, VERSION 3.3.1<br>> Source code file: trnio.c, line: 69<br>> Fatal error:<br>> Float size 401. Maybe different CPU?<br>><br>> I am using gromacs 3.3.1. Also I am wondering there is any new
<br>> update on the extration of C-alpha modes based on the all-atom<br>> Hessian matrix? Thanks for the help.<br><br>We had to discard the old Hessian format when introducing the sparse<br>matrix representation to enable NMA for huge molecules. The easiest
<br>way to extract the data is probably to have a look in src/tools/<br>gmx_nmeig.c.<br><br>As for C-alpha modes, projections of orthogonal vectors onto a<br>subspace won't be orthogonal in that subspace, so per definition they
<br>are not "normal" modes for C-alpha. If you really want Ca-only modes<br>you are probably better of with an elastic network model online<br>server, e.g. <a href="http://lorentz.immstr.pasteur.fr">http://lorentz.immstr.pasteur.fr
</a> .<br><br>Cheers,<br><br>Erik<br><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
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