[gmx-users] Representative structure from MD trajectories

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Sep 10 10:05:26 CEST 2011

Hi Bipin,

The averages from (2) and (3) are the same and may be far from realistic.
Minimizing an average structure may not always yield a structure that is
relevant or representative of the ensemble. I would suggest clustering
But you should only have a limited number of structures for a given point
(pc1,pc2), so why not just visualize the ensemble?

Hope it helps,


On Sep 10, 2011 8:02 AM, "bipin singh" <bipinelmat at gmail.com> wrote:


I have constructed a 2-d FEL using PC1 and PC2 as the reaction
coordinates(by using g_sham).
>From this 2-d FEL, I extracted the PC1 and PC2 (principal components)
values corresponding to minimum free energy.
Then I extracted the time during which system possess these PC's
values( by looking at PC Vs time plot).
Now I want to extract representative structures from these time
length(for eg. 40ns to 70 ns) of MD trajectories.

This question had been discussed previously but I am not able to find
a consensus solution:

There are three approaches discussed in the previous posts:
(1)Use g_cluster with options -av(writes average) -cl and then
minimize the structure
(2)Use g_covar -av, and then minimize the average structure.
(3)Use g_rmsf -ox, and minimize the structure

Please suggest which approach should be used for this purpose.

Thanks and Regards,
Bipin Singh
gmx-users mailing list    gmx-users at gromacs.org
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110910/c237bec0/attachment.html>

More information about the gromacs.org_gmx-users mailing list