Re: Writing 3 subsequent timesteps to the DCD file

From: Axel Kohlmeyer (
Date: Wed Apr 08 2009 - 08:23:26 CDT

On Wed, 2009-04-08 at 12:44 +0300, Mert Gür wrote:
> Writing every 1 step gives me an huge DCD which is hard to handle even
> for short simulation times.
> How about I perform 3 simulations at the same time.

won't work. particularly, if you run the individual runs
as parallel jobs.

> I have a previous simulation and I will use its restart files so that
> my initial system conditions are specified.
> 1- First simulation I run with a DCD frequency of every 100th step
> 2-For the second simulation, I first run my simulation for 1 step and
> then use the final restart files for my second simulation and get the
> DCD frequency every 100th step
> 3--For the third simulation I first run my simulation for 2 step and
> then use the final restart files for my third simulation and then get
> the DCD frequency every 100th step.
> So I need these simulations to be identically the same so that I will
> get the consequent coordinates as I desire. In other words the 100.
> step of my first simulation should be the 99. of the second and the
> 98. of the third.
> As much as my understanding goes that should be possible. In case it
> is what do I have to be carefull about?

please update your understanding. it has been discussed on this list
many times that subsequent (parallel) runs are sampling the same
ensemble, but are not guaranteed to be binary identical. due to
inherently divergent nature of coupled partial differential equations,
that you (only) solve numerically, trajectories will always diverge

again, if you would explain _why_ you need this strange output
frequency, perhaps somebody can suggest an alternate solution.
as it stands, you have no choice but to modify the NAMD source
code and introduce your own flag for your purposes.

> Would it be enough if I set only the following parameters to 1?
> nonbondedFreq 1
> fullElectFrequency 1
> stepspercycle 1

this would be _very_ wasteful as you would not only run the same
simulation 3 times, but also run each of them highly inefficiently.
and yet it would still not sufficient. if you want this output so
badly, you better get your preferred text editor and compiler ready
and attack the sources.


> Best,
> Mert
> On Tue, Apr 7, 2009 at 2:24 PM, Mert Gür <> 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. timesteps and then for the 200., 201, 202. time step
> and then again for the 300., 301. ,302, timesteps and so on...
> Can I do that?
> Any suggestion or even alternative ways to do that would be of
> big help to me.
> Best,
> Mert
> Center for Computational Biology and Bioinformatics
> Koc University
> Sariyer 34450, Istanbul, Turkey

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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