Dear Gromacs users,
I am analyzing the RMSD evolution of a trajectory with g_rms and
clustering it with g_cluster (GROMOS, cutoff 0.1). I am noticing
something quite odd in the RMSD distribution. I link here the RMSD
evolution over time , the cluster ID over time, and the RMSD
distribution
Hi Massimo,
You have two clusters, both with low within-cluster RMSD. This shows up as
the first peak in the RMSD distribution. The second peak is the
between-clusters RMSD.
Cheers,
Tsjerk
On Wed, Aug 13, 2014 at 3:14 PM, ms deviceran...@gmail.com wrote:
Dear Gromacs users,
I am
Hi Tsjerk,
On 8/13/14 3:19 PM, Tsjerk Wassenaar wrote:
You have two clusters, both with low within-cluster RMSD. This shows up as
the first peak in the RMSD distribution. The second peak is the
between-clusters RMSD.
I am sorry, but I don't understand anything here - what does
within-cluster
H Massimo,
The RMSD over time is the RMSD against a single reference structure. For
clustering you use the RMSD matrix, which has all pairwise RMSDs. The
distribution you show is the distribution of RMSD values in that matrix.
Cheers,
Tsjerk
On Wed, Aug 13, 2014 at 3:44 PM, ms
On 8/13/14 4:01 PM, Tsjerk Wassenaar wrote:
H Massimo,
The RMSD over time is the RMSD against a single reference structure. For
clustering you use the RMSD matrix, which has all pairwise RMSDs. The
distribution you show is the distribution of RMSD values in that matrix.
Aha! This makes much
On 8/13/14, 10:11 AM, ms wrote:
On 8/13/14 4:01 PM, Tsjerk Wassenaar wrote:
H Massimo,
The RMSD over time is the RMSD against a single reference structure. For
clustering you use the RMSD matrix, which has all pairwise RMSDs. The
distribution you show is the distribution of RMSD values in
On 8/13/14 4:17 PM, Justin Lemkul wrote:
Aha! This makes much more sense then, thanks!
Is there a Gromacs command to get the histogram of RMSD against a single
reference structure, then?
You can construct histograms of any time series with g_analyze -dist.
OK, I forgot that. Thanks a lot,
