From: Shirley Hui (s2hui_at_hotmail.com)
Date: Wed Jun 08 2005 - 12:45:04 CDT
Hi,
You can remove rotational and translational degrees of freedom by reading in
the DCD files into Matlab, for each structure, peform a rigid structure
alignment with one of the molecules in the trajectory.
How to read in DCD using matlab:
http://www.ks.uiuc.edu/Development/MDTools/matdcd/
Perform a rigid alignment using matlab via SVD:
http://www.public.iastate.edu/~hyao/RMSD.m
Read the structures back into DCD format using MatDCD again.
Matlab has limitations on how large input files can be though, so this may
or may not work depending on how large your DCD file is.
This approach to remove rotational and translational degrees of freedom iis
based on methods used widely in literature.
shirley
>From: Leonardo Sepulveda Durán <leonardosepulveda_at_gmail.com>
>Reply-To: Leonardo Sepulveda Durán <leonardosepulveda_at_gmail.com>
>To: namd-l_at_ks.uiuc.edu
>Subject: namd-l: Avoiding Rotation and translation of protein
>Date: Wed, 8 Jun 2005 11:58:33 -0400
>
>Hello!!!!!
>
>I am performing a NPT dynamics of a protein. I use a 10A waterbox, and
>2 ions (neutral system), PBC and PME. At 400 ps, the protein begins to
>rotate (I dont Know if its center of mass translates too),
>furthermore, one residue comes dangerously close to the border of the
>box. I would like to ask if there is a way to avoid such protein
>movements in the simulation, or whether there is a way to reorganize
>trayectory files later in order to obtain a dcd where this movements
>are taken out. And if that is posible, what happens if one of my
>protein's residue steeps through th boundary? Is that Dynamics lost???
>
>Thanks
>
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