Thank you very much.
2012/4/20 Jan-Philip Gehrcke <jgehrcke.googlemail.com>:
> Fabrício,
>
> after having created your data file using cpptraj, it contains a 'frame
> number' column and a 'value' colum, right? You now need an automatic
> conversion between 'frame number' and 'time'.
>
> I.e., for instance from
>
> frame value
> 1 3.1415
> 2 1.3337
>
> to
>
> time/ns value
> 0.005 3.1415
> 0.010 1.3337
>
> You can use the data file created by cpptraj and use your favourite
> programming language to do this conversion. A quick&dirty Python script
> doing this is attached. Maybe you can use it for your case without
> modification. The modified data is written to stdout, so in order to create
> a new data file with the time instead of frame number, you would have to
> redirect stdout to a file, e.g.
>
> $ python ptrajrms_convert_frame_to_time.py 0.002 rms_over_framenumber.dat >
> rms_over_time.dat
>
> Hope this helps,
>
> Jan-Philip
>
>
>
> On 04/20/2012 04:25 PM, Fabrício Bracht wrote:
>>
>> Hi Liu. I read the documentation on cpptraj. The problem is that the
>> {offset} mask is not exactly what I need. The thing is: my trajectory
>> was written every 2ps. When cpptraj reads the trajectory (for
>> instance, while doing secstruct) it writes a file that has on the x
>> axis the number of frames and not the amount of ps that were
>> simulated. For example, if I simulate 10000 ps saving every 2ps,
>> cpptraj will write a graph from 0 to 5000. In this case, I actually
>> have all 5000 frames on the graph, but it does not correspond to my
>> simulation time. The offset mask will simply skip frames, not
>> analysing them at all. With ptraj, when I specify the 'time' variable,
>> it understands that my simulation was written every 2 ps. So in this
>> case, does it mean that I will have to write a script to change the
>> frame values to match my simulation time?
>> Was this too confusing? I don't know if I was clear enough. Please let
>> me know if I'm being too confusing.
>> Thank you
>> Fabrício
>>
>> 2012/4/19 Liu Denis<cndenis.gmail.com>:
>>>
>>> Hi Fabricio：
>>> Cpptraj is well documented in AmberTools 12 manual. The syntax of
>>> trajin in cpptrj is similar to the one in ptraj.
>>> Please refer to Page 171, I copied it here:
>>>
>>> trajin<filename> [<start> [[<stop> | last] [<offset>]]] | lastframe
>>> [parm<parmfile> | parmindex<#>]
>>> [remdtraj remdtrajtemp<Temperature> remdout<outprefix> [netcdf]
>>> trajnames<Comma-separated name list>]
>>>
>>> Read in trajectory specified by filename. Currently Cpptraj will
>>> recognize
>>> Amber trajectories,
>>> Amber Netcdf Trajectories, Charmm DCD trajectories, Amber Restart files,
>>> PDB files, and
>>> TRIPOS MOL2 files. The frames to be read in can be specified with the
>>> <start>,<stop>, and
>>> <offset> arguments (defaults are first frame, last frame, and 1
>>> respectively). If just the<start>
>>> argument is given, all frames from<start> to the last frame of the
>>> trjaectory will be read. To
>>> read in a trajectory with offsets where the last frame # is not known,
>>> specify thelast keyword
>>> instead of a<stop> argument, e.g.
>>>
>>> trajin Test1.crd 10 last 2
>>>
>>> This will process Test1.crd from frame 10 to the last frame, skipping by
>>> 2
>>> frames. To explicitly
>>> select only the last frame, specify thelastframe keyword:
>>>
>>> trajin Test1.crd lastframe
>>>
>>> 2012/4/20 Fabrício Bracht<bracht.iq.ufrj.br>
>>>
>>>> Is there a way to define the time interval using cpptraj. In ptraj all
>>>> you have to do is define " time<time interval> " in the config file,
>>>> but I haven't found any mention about this with cpptraj.
>>>> Thank you
>>>> Fabrício Bracht
>>>>
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>>>
>>>
>>>
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Received on Fri Apr 20 2012 - 11:30:02 PDT
