From: Mert Gür (gurmert_at_gmail.com)
Date: Wed Apr 08 2009 - 14:36:45 CDT
Dear all,
I really appreciate all the effort you have provided to help me. I am trying
to find a solution in the light of the suggestion you have given me. Since
my question diverged to a different point I also posted it as a new
question.
Best,
Mert
On Wed, Apr 8, 2009 at 9:40 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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