**From:** Axel Kohlmeyer (*akohlmey_at_cmm.chem.upenn.edu*)

**Date:** Fri Apr 10 2009 - 12:02:06 CDT

**Next message:**JT: "Re: Evaluating kinetic energy from a modified DCD file"**Previous message:**Mert Gür: "Re: Writing 3 subsequent timesteps to the DCD file"**In reply to:**Mert Gür: "Re: Writing 3 subsequent timesteps to the DCD file"**Next in thread:**Giacomo Fiorin: "Re: Writing 3 subsequent timesteps to the DCD file"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

On Fri, Apr 10, 2009 at 10:24 AM, Mert Gür <gurmert_at_gmail.com> wrote:

*> Dear Axel,
*

*> Your following suggestion:
*

*>
*

*> "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?"
*

*>
*

*> was the best sounding suggestion to me. But I am not sure if I will be able
*

*> to do it perfectly the same way the analysis code is doing it.
*

*> Another question, maybe its silly but it came to my mind. Can I write
*

*> multiple dcdfiles in NAMD?
*

*>
*

*> Dear David and Grace,
*

*> I need the velocities of each mode. The velocity dcd will give me the
*

*> velocities of all modes superposed on each other. This is my problem . I
*

*> need each velocity after I have gone back for each mode which I do by
*

*> generating a dcd file for each mode.
*

mert,

nothing keeps you from projecting the velocites on the individual mode(s).

that should give you the information you want right away.

cheers,

axel.

*>
*

*> Best,
*

*> Mert
*

*>
*

*>
*

*>
*

*> On Thu, Apr 9, 2009 at 1:36 AM, Grace Brannigan <gracebrannigan_at_gmail.com>
*

*> wrote:
*

*>>
*

*>> Hi Mert,
*

*>>
*

*>> The "output files" section of the namd user's guide will tell you how to
*

*>> write a velocity dcd file. It sounds like this is all you need.
*

*>>
*

*>> -Grace
*

*>>
*

*>> On Wed, Apr 8, 2009 at 2:40 PM, Mert Gür <gurmert_at_gmail.com> wrote:
*

*>>>
*

*>>> 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/
*

*>>>> >
*

*>>>> >
*

*>>>> >
*

*>>>> >
*

*>>>> >
*

*>>>> >
*

*>>>>
*

*>>>> --
*

*>>>> =======================================================================
*

*>>>> 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.
*

*>>>>
*

*>>>
*

*>>
*

*>
*

*>
*

-- ======================================================================= 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.

**Next message:**JT: "Re: Evaluating kinetic energy from a modified DCD file"**Previous message:**Mert Gür: "Re: Writing 3 subsequent timesteps to the DCD file"**In reply to:**Mert Gür: "Re: Writing 3 subsequent timesteps to the DCD file"**Next in thread:**Giacomo Fiorin: "Re: Writing 3 subsequent timesteps to the DCD file"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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