Enjoy! I would spend 30-60 minutes modifying the fortran.
Bill
On 8/28/17 12:26 AM, Jewgeni Starikow wrote:
> 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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Received on Mon Aug 28 2017 - 02:00:03 PDT
