Re: Writing 3 subsequent timesteps to the DCD file

From: Mert Gür (gurmert_at_gmail.com)
Date: Wed Apr 08 2009 - 13:40:43 CDT

To be more specific ,my problem is that:
I am first doing modal decomposition . By keeping selected modes (for
example only the first mode) I go back to the cartesian coordinates and
generate a dcd file. Using this DCD file I am trying to evaluate the
potential energies and the kinetic energies of the selected modes.
 If I am not mistaken , NAMD energy plugin gives me the potential energy
with respect to this DCD file.
But to evaluate the kinetic energy, I was planning to use the coordinates of
the previous and succesive time frames. Using this frames I am going to
evaluate the velocity and hence the KE.
This is where I am stuck now.
Mert

On Wed, Apr 8, 2009 at 6:26 PM, Axel Kohlmeyer
<akohlmey_at_cmm.chem.upenn.edu>wrote:

> On Wed, 2009-04-08 at 09:33 -0500, David Hardy wrote:
> > I've got a suggestion.
> >
> >
> > Run a simulation that produces a saved binary restart file every 100
> > steps, then do post-processing in which you start a NAMD simulation
> > that runs for just 2 steps from each of the binary restart files to
> > produce a DCD file, then join the resulting DCD files together. You
> > might have to adjust this recipe because I recall that DCD files don't
> > store the zeroth frame.
>
> one more - simpler - option along those lines:
> how about saving the velocities and positions at the same frame
> and then just reconstruct the step before and after the given positions
> by doing one velocity verlet step each forwards and backwards in the
> analysis code?
>
> axel.
>
>
>
> >
> >
> > Best regards,
> > Dave
> >
> >
> >
> > On Apr 8, 2009, at 8:23 AM, Axel Kohlmeyer wrote:
> >
> > > 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
> > > exponentially.
> > >
> > >
> > > 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.
> > >
> > >
> > > cheers,
> > > axel.
> > >
> > >
> > > >
> > > >
> > > > Best,
> > > > Mert
> > > >
> > > >
> > > >
> > > >
> > > > On Tue, Apr 7, 2009 at 2:24 PM, 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. 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 akohlmey_at_cmm.chem.upenn.edu
> > > http://www.cmm.upenn.edu
> > > 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.
> >
> >
> >
> >
> > --
> > David J. Hardy, Ph.D.
> > Theoretical and Computational Biophysics
> > Beckman Institute, University of Illinois
> > dhardy_at_ks.uiuc.edu
> > http://www.ks.uiuc.edu/~dhardy/ <http://www.ks.uiuc.edu/%7Edhardy/>
> >
> >
> >
> >
> >
> >
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> 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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