[gmx-users] MD on a protein region

deepa rajamani deepsri at bu.edu
Mon Apr 18 21:57:54 CEST 2005


I am trying to run MD on a region of protein. I tried the following things
1. Made a huge box, centered the protein and then filled the box with
water and included freeze groups in the mdp file.
	problem: The run is not short enough, since all the water
molecules in the huge box is moving anyway

2. Made a small box which sees only an indexed group of atoms and filled
that box with water.
	problem: similar to chopping the protein, the atoms seem to be
rotating a lot, the run does not get completed since the atoms move a
producing a huge rmsd and huge rotations (gives me error like rotated

What would be the best way to do a quick run on a part of the protein

Deepa Rajamani

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