From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Apr 10 2009 - 12:02:06 CDT
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.
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