From: Mert Gür (gurmert_at_gmail.com)
Date: Fri Apr 10 2009 - 10:24:23 CDT
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.
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/ <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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