Hi,
Oh ok, thanks! That is super helpful, but I have two short followup questions. Does LES
split only work when I convert the LES coordinate file into a standard amber coordinate file, as
opposed to a pdb? I'm only asking because I only get 100 trajectories from the script that
I used, and it seems like I should have gotten more (#LES copies * 100). Also, if I have a LES simulation with
3 regions and 5 copies each, will the LES split function split this into 15 different non-LES
trajectories that I would later have to process?
Thanks,
Jim
----- Original Message -----
From: "Daniel Roe" <daniel.r.roe.gmail.com>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Sunday, August 11, 2013 11:20:19 AM
Subject: Re: [AMBER] ptraj is not splitting LES trajectory
Hi,
It seems that the description of 'trajout les split' in the manual is
not correct. It states:
'The “split” key-word will output N separate trajectories, one for
each LES group...'
However, what it actually does is output a single trajectory where the
LES groups have been separated by frame. So say for example you had 3
copies of an LES group (call them a, b, c) in an LES trajectory with 5
frames. After the 'trajout les split' command you will have a
trajectory with 15 frames, where each LES frame has been split by
group, like so:
1a 1b 1c 2a 2b 2c 3a 3b 3c 4a 4b 4c 5a 5b 5c
The new trajectory can be processed with your original (i.e. non-LES)
topology. You can verify this visually using your favorite MD
visualization software. You can use start/stop/offset 'trajin' args to
access only a specific group; for example, to process only group 'b'
in the above example you could use 'trajin <filename> 2 14 3'.
One more note: I would be very cautious in doing *any* actions on the
LES trajectory before it is split or averaged. For example, in your
original script you have 'center .CA origin mass'. If in your LES
region you have CA atoms this will skew the centering calculation
since there are multiple copies of the atoms in that region. It's
probably best to first split or average, then do any actions.
Hope this helps,
-Dan
PS - I am in the process of adding the LES functionality to cpptraj,
where it can be processed as an ensemble (similar to the way REMD
trajectories can currently be processed as an ensemble). This should
make splitting and analyzing LES trajectories simpler. However, this
will require lots of testing and verification before release so
unfortunately I don't have a timetable for this functionality yet.
On Fri, Aug 9, 2013 at 7:09 PM, James W. Snyder, Jr.
<jsnyder3.stanford.edu> wrote:
> Hey,
>
> Thanks for the quick reply! I tried other file formats, like the amber coordinate
> file format. This didn't seem to solve the problem.
>
> Thanks,
>
> Jim
>
> ----- Original Message -----
> From: "Daniel Roe" <daniel.r.roe.gmail.com>
> To: "AMBER Mailing List" <amber.ambermd.org>
> Sent: Friday, August 9, 2013 5:59:12 PM
> Subject: Re: [AMBER] ptraj is not splitting LES trajectory
>
> Hi,
>
> I don't have a lot of experience with LES trajectories, but does it
> work if you try to output to a different trajectory format, and/or
> omit the append keyword?
>
> To my knowledge the LES trajectory processing capability of ptraj
> hasn't been tested in a while, so it's possible some bugs have crept
> in there. I will try and test this over the next day or so and let you
> know what I find. Thanks for the report.
>
> -Dan
>
> On Fri, Aug 9, 2013 at 6:02 PM, James W. Snyder, Jr.
> <jsnyder3.stanford.edu> wrote:
>> Hey,
>>
>> I am trying to use ptraj to split my sander.LES trajectory into multiple trajectories
>> based on the number of copies. However, I am only getting a single output file that
>> corresponds to either just one copy or an average of all the copies. Here is my
>> ptraj input...
>>
>> trajin gfp_wt_les1.mdcrd 100 10000 100
>> center .CA origin mass
>> image origin
>> trajout output.pdb pdb append les split
>>
>> Does anyone have a solutions to this problem?
>>
>> Thanks,
>>
>> Jim Snyder
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Sun Aug 11 2013 - 13:00:03 PDT
