Re: Writing 3 subsequent timesteps to the DCD file

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Apr 07 2009 - 19:45:45 CDT

On Tue, 2009-04-07 at 19:53 -0400, JT wrote:
> Well, it might take alot of disk space, but you can do it by telling
> NAMD to write out every step into the output DCD, then use catdcd to
> splice together the desired trajectory.

that would be _very_ inefficient and can easily
flood file systems.

> On Apr 7, 2009, at 3:29 PM, Goutham wrote:
>
> > I thought NAMD can read TCL scripts in the config file.. Wouldn't
> > that work?
> > A tcl script to modify the dcd write frequency?

in general, it is difficult to modify input parameters, once
a calculation is started. you would have to re-initialize most
of the internal data structures. not very efficient.

before speculating any further, it might be helpful to learn
what the application would that that requires such an unusual
output frequency.

cheers,
   axel.

> >
> > On Tue, Apr 7, 2009 at 5:45 AM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> > wrote:
> >
> >> On Tue, Apr 7, 2009 at 6:24 AM, Mert Gür <gurmert_at_gmail.com> wrote:
> >>> Hi everyone!
> >>>
> >>> I want to write the coordinates of 3 subsequent time frames into
> >>> my DCD
> >>> file.
> >>>
> >>> For example
> >>>
> >>> Lets say I have a DCD writing frequency of every 100th step. Hence
> >>> I am
> >>> writing the coordinates for the 100.time step and then for the 200.
> >>> timestep......
> >>>
> >>> But what I need to do is to write my coordinates for the 100.,
> >>> 101, 102

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
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