[gmx-users] Handling a very large system

Ken Rotondi ksr at chemistry.umass.edu
Thu Jul 21 21:55:16 CEST 2005

Dear All,

As you can imagine based upon my recent questions, I am  simulating 
(trying to) a very large system. I'm interested in removing as many 
degrees of freedom from the system as possible, as well as minimizing 
the data storage pressures. To this end I'd like to do the following:

1) Make the aromatic rings in my simulation ridged. From chapter 6 I 
gather that this is done using the pdb2gmx flag -dummy aromatic. I have 
two questions:  is this correct? (if not is this possible and how?) Is 
it possible to do this with the aromatic portions of DNA and RNA bases?

2) I can constrain all angles in the system using:

  constraints = all bonds

in my .mdp file. Is it possible to apply these restraints to a sub-set 
of all residues in the system?

3) This is a long-shot or worse. Using trjorder one can order the 
solvent molecules by their distance from the proteins. Is there anyway 
to, on the fly, store only the n-closest waters each time the 
coordinates are saved during a trajectory?

Thank you all very much in advance,

K.S. Rotondi Ph.D.
Research Fellow
The Gierasch Laboratory
Department of Biochemistry and Molecular Biology
University of Massachusetts-Amherst
Phone: 413-545-1250
Fax;      413-545-3291

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