[gmx-users] Handling a very large system

[David]

On Thu, 2005-07-21 at 15:55 -0400, Ken Rotondi wrote:
> 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?
No, and we do not recommend the -dummy aromatic flag right now, since we
are not confident that the dynamics is OK. With -dummy h you can take 4
fs timesteps.

> 
> 2) I can constrain all angles in the system using:
> 
>   constraints = all bonds
this would constrain bonds only, which is fine. constraining angles
gives problems with the LINCS algorithm although it may work with SHAKE.

> 
> 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?
No.

> 
> Thank you all very much in advance,
> 
> Ken
> 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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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