[gmx-users] FEL generated by dPCA and radius of gyrationa vs RMSD

David van der Spoel spoel at xray.bmc.uu.se
Mon Jun 18 13:59:26 CEST 2018

Den 2018-06-18 kl. 12:04, skrev Seera Suryanarayana:
> Dear gromacs users,
> I have generated free energy landscape by two methods such as dPCA and
> radius of gyration vs RMSD to average structure. In dPCA  I got less number
> of meta conformational states than radius of gyration vs RMSD method. Can I
> use the second method for my paper submission?
> Thanks in advance
> Surya
> Graduate student
> India.
You have to compare the two, in particular you have to analyze what the 
dPCA states mean in cartesian space. They may be very similar.

Then you have to ask yourself the question whether the results have any 
predictive value that can be evaluated experimentally...

David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.

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