[AMBER] Regarding RMSD calculation and Clustering

From: Manish Kumar Mohanty <mkmohanty.iiserb.ac.in>
Date: Sun, 9 Feb 2020 10:40:09 +0530

Dear AMBERites,

I am very new to AMBER and currently using AMBER 18. So, please forgive me,
if my questions are too basic.

1- Before RMSD calculation and clustering, I used the following code in
cpptraj to remove all translational and rotational motions of DNA
moiety during the simulation, according to the link:
https://amberhub.chpc.utah.edu/combining-multiple-trajectory-files-into-a-single-trajectory-and-remove-water-molecules-to-save-space/
 *parm topology-file.prmtop*
* trajin trajectory*.nc 1 last 10 *
* autoimage*
* strip :WAT *
* rms fit :1-24*
* trajout nowater.nc <http://nowater.nc>*
* go *

Now, if I want to do rmsd calculation for the DNA 12-mer, will the data
present in nowater.nc be fine? Or should I use this and proceed?
* rms ToFirst :1-24&!.H *

If possible, can someone clarify the difference between *rms fit* and* rms
ToFirst* command?
*2- *I have a single trajectory of 1 ╬╝sec long DNA duplex simulation. Is it
reliable to do clustering for the same after RMSD calculation to sample all
the possible conformations or should clustering be done for multiple
trajectories using different starting structures only? Then is it ok to do
Markov State Modelling using the clusters obtained?

Thanks
Manish
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Received on Sat Feb 08 2020 - 21:30:01 PST
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