Re: [AMBER] I have generated an AMBER trajectory with coordinates, velocities and forces. How can I place the relevant data sets in the text file?

From: Jewgeni Starikow <>
Date: Mon, 28 Aug 2017 15:45:45 +0200

Dear Dan,

many sincere thanks for your prompt and truly helpful response!

In fact, I wouldn't like to add solely 'dumping' functionality to
CPPTRAJ, just to produce further output files.

My actual idea would be as follows:

I would greatly appreciate EXTRACTING the already generated
coordinate/velocity/force data from the NetCDF trajectory file to place
them into some allocated memory areas, and work with them on the fly, so
to speak.

In particular, I would like to look for the generic regression (e.g.,
some kernel regression) of the Forces and Velocities onto the
Coordinates. This way, I expect getting the direct information as for
the kinetic and potential energies of the system under study in 'their
temporal development', so to speak.

Obtaining such an information ought to allow me learning about the
generic capabilities of the polymeric system under study, when it is
placed on the surface, into the nanoscopic 'cups' etc.

Getting the infos concerning the systems 'energetics', so to speak, is
the first step, whereas the second important step ought to be the
so-called factor analysis of the correlations among the atoms of the
system and its couterion-water sheath. With this information at hand you
might decide about the roles of the protein/DNA/sugar domains, the
couterion-water sheath in the processes you are studying.

We have already applied such an approach (though, without the
above-mentioned energetics!) to study the modalities of cyclodextrins'
solubility in water:

With all this in mind I shall definitely add such a feature request to
the cpptraj GitHub page... Moreover, I am presently thinking about the
actual regression routines. The factor analysis of large & sparse
correlation matrices might be accomplished with the routines from the
ARPACK library, for example... Howbeit, I would anyway be ready for
active collaborations with the CPPTRAJ authors...

Respectfully yours,


On 2017-08-28 14:39, Daniel Roe wrote:
> Hi,
> What you want to do is currently not entirely possible with cpptraj.
> Getting the coordinate/velocity/force data could potentially be done
> but it's not straightforward.
> I assume the trajectory is in NetCDF format. FYI NetCDF distributions
> come with a tool called 'ncdump' which can be used to extract values
> from NetCDF files in text format. For example:
> ncdump -v coordinates <file>
> can be used to extract the coordinates from an Amber NetCDF
> trajectory
> file. 'ncdump -h <file>' can be used to see which variable names are
> present in the file.
> If you would like this functionality to be a part of cpptraj feel
> free
> to add a feature request to the cpptraj GitHub page:
> -Dan
> On Sun, Aug 27, 2017 at 5:41 PM, Jewgeni Starikow
> <> wrote:
>> Dear all,
>> I have generated an AMBER trajectory with coordinates, velocities
>> and
>> forces at every time point. It is readily readable with the standard
>> CPPTRAJ routine.
>> Now, from this point on, how could I write out the relevant data
>> sets
>> in some (text or binary) file readable in some straightforward way?
>> I would greatly appreciate ordering my corresponding output file
>> like
>> as follows:
>> Atom-Nr Time CoordX CoordY CoordZ VelocX VelocY VelocZ
>> ForceX ForceY ForceZ
>> ... ... ... ... ... ... ... ...
>> ... ... ...
>> ...etc., etc., etc. ...
>> Which set of the CPPTRAJ commands would be most appropriate for the
>> above-outlined case?
>> Respectfully yours,
>> Evgeni B. Starikov
>> _______________________________________________
>> AMBER mailing list

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Received on Mon Aug 28 2017 - 07:00:02 PDT
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