Dear Bill,
...sure, I see the point and am in effect not a big fan of Python
(which is to my mind nothing more than just a transformation of the old
and good C++ && Java). What I am thinking about ought to be not
transforming/extending the Amber itself, but, instead,
transforming/extending the CPPTRAJ. The latter routine is already a very
useful tool, but I would greatly appreciate adding one more capability
to it. Then, there ought to be no need in producing the
coordinate-velocity-force data files for reading them anew. In effect, I
would strive for working with these data sets on the fly, so-to-speak...
I have already shared my idea with Thom Cheatham, the main author of
the CPPTRAJ, but to my regret, there had been no reaction from him -
maybe due to summer holidays??? ... The reaction from his group would be
of extreme interest for the story, for they have written the code, so
that myself I shall definitely spend months, or so, in trying to
successfully transform/extend it...
Respectfully yours,
Evgeni
On 2017-08-28 08:16, Bill Ross wrote:
> Hi Evgeni,
>
> Python sounds cool too, but it'll always be one extra thing to run.
>
> Bill
>
>
> On 8/27/17 10:24 PM, Jewgeni Starikow wrote:
>> Dear Bill,
>>
>>
>> ...many sincere thanks, that's what I am just thinking about
>> myself...
>>
>>
>> Respectfully yours,
>>
>> Evgeni
>>
>> On 2017-08-28 00:38, Bill Ross wrote:
>>> I recommend adding your own output routine to the program
>>> (sander/pmemd)
>>> to write the desired format directly, after looking at the other
>>> file
>>> output routines.
>>>
>>> Bill
>>>
>>>
>>> On 8/27/17 2:41 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
>>>>
>>>> _______________________________________________
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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
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>>
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>
>
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Received on Mon Aug 28 2017 - 00:30:02 PDT
