From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Aug 13 2010 - 08:54:51 CDT
On Fri, 2010-08-13 at 09:06 -0400, Lisa Brown wrote:
> Thank you Thanassis and Nabil.
> But I need it BEFORE the simulation. I want to do a simulation in a
> solvated system, but I do not need water coordinates in my DCD file at
> seems to be there's no way .
there _always_ is a way. the question is: do you want
to invest the effort walk it? for example:
you could change the namd source code.
you could use LAMMPS-ICMS instead of NAMD,
which does supports output of dcd for subsets of
a system _and_ also support this for compressed .xtc
trajectories, which might be even more interesting, if you
are concerned about disk usage. the problem with LAMMPS
is that its parallel performance for typical bio systems
is about half of NAMD, and it supports a different feature
set than NAMD. i'm working on improving its parallel performance,
but since it is designed to be far more general, there are
limitations that are impossible to overcome.
> anyway thank you for the help.
> 2010/8/12 Athanassios Stavrakoudis <astavrak_at_cc.uoi.gr>:
> > Hi Lisa,
> > NAMD will store the coordinates of all atoms.
> > If you want to get rid of the solvent, AFTER the simulation,
> > then Carma or Eucb or catdcd packages might help you:
> > http://utopia.duth.gr/~glykos/carma.html
> > http://stavrakoudis.econ.uoi.gr/eucb
> > http://www.ks.uiuc.edu/Development/MDTools/catdcd/
> > Best,
> > Thanassis
> >> Hi all,
> >> I have a solvated system,need to run long simulations using NAMD and
> >> want to save only the protein coodinates in my DCD file.
> >> I searched about this but could not find anything related to saving
> >> DCD files without water moelcule coordinates.
> >> I will greatly appreciate, if someone help me with this.
> >> Thank you in advance
> >> Lisa
> > Athanassios Stavrakoudis
> > University of Ioannina web: http://stavrakoudis.econ.uoi.gr/
> > Department of Economics e-mail: mailto:astavrak_at_cc.uoi.gr
> > GR-45110, Ioannina tel: +30 265 100 5935
> > GREECE fax: +30 265 100 5092
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://sites.google.com/site/akohlmey/ Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
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