<DIV>Thank you very much.</DIV>
<DIV> </DIV>
<DIV>The significant conformation changes occurred between 3.3ns and 3.9ns, which I am interested for. The cosine content in this 0.6ns is low (just 0.29; calculated by "g_analyze -f proj5ns.xvg -cc proj5ns_cc.xvg -b 3300 -e 3890"); I want to know whether it indicates that the movement of protein IN THIS 0.6ns is believable? </DIV>
<DIV> </DIV>
<DIV> </DIV>
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<BR>-----Original Message-----<BR>From:"David van der Spoel" <SPOEL@XRAY.BMC.UU.SE><BR>Sent:2006-09-11 09:20:33<BR>To:"M. Yan" <YANMAOCAI@126.COM><BR>Title :Re: [gmx-users] May I use "-b" and "- e" in the cosine con tent calculation of PC?<BR><BR><BR><PRE style="WIDTH: 100%; WORD-WRAP: break-word">M. Yan wrote:
> Hi,
> In fact I simulated 30 nanoseconds, but I found the system reached
> equilibrium at 4.4 ns (by analyzing RMSD, Energy and visualizing,
> etc.) and did not change significantly in the last 25 ns. Thus I want to
> do an essential dynamics for the first 5 ns.
> I also calculated the covariance matrix for the whole 30 nanoseconds,
> but the cosine content of PC1 is still as high as 0.710. However, MD
> simulation longer than 30 ns is beyond our compute ability. Then what
> shall I do?
>
> Thanks.
>
>
>
>
Try ED of the last 25 ns only. The first 5 represent equilibration and
unless you are specifically interested in th force field issues etc.
related to that, you should discard those 5 ns for analysis.
Then try to do other analyses as well and try to make sense of the whole
simulation. IIRC the cosine content being high indicates that the
protein performs a random walk on a relatively flat free energy surface.
This is informative in itself but needs to be considered in the context
of additional analysis and the background of your investigation.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel@xray.bmc.uu.se spoel@gromacs.org <A href="http://folding.bmc.uu.se/" target=_new>http://folding.bmc.uu.se</A>
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