On Tue, Sep 20, 2016 at 11:01 AM, Samuel Bowerman <sbowerma.hawk.iit.edu> wrote:
> Wow, thanks for being so diligent in tracking this bug down! I have been
> slowly whittling down my trajectories due to finite memory issues and was
> just about to begin post-processing the atommaps again, so your fix is
> perfectly timed. Thanks!
Glad to hear - I tested somewhat thoroughly so this should be good to
go but let me know if you encounter any more strangeness.
-Dan
>
> Take care,
> Samuel Bowerman
> Ph.D. Candidate
> Department of Physics
> Illinois Institute of Technology
>
> On Tue, Sep 20, 2016 at 9:06 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> I was able to track down the bug - in 'crdaction' where the action
>> modified the topology, the wrong frame was being passed in leading to
>> memory issues. I've fixed the issue in GitHub and will work on a patch
>> for AmberTools. If you use the GitHub version the script previously
>> posted should work fine now. Thanks for the report and the files!
>>
>> -Dan
>>
>> On Wed, Aug 31, 2016 at 9:12 AM, Daniel Roe <daniel.r.roe.gmail.com>
>> wrote:
>> > Hm - sounds like a potential bug. Would you mind sending me off-list some
>> > files I could use to reproduce this behavior (sounds like trajectories
>> only
>> > need to be 2 frames to see the problem).
>> >
>> > I am currently in the middle of a move so I may not be able to get to
>> this
>> > as soon as I would like, but if there is a problem I'd eventually like to
>> > correct it.
>> >
>> > Glad to hear you could still do the analysis you wanted.
>> >
>> > -Dan
>> >
>> >
>> > On Tuesday, August 30, 2016, Samuel Bowerman <
>> sbowerma+amber-l.hawk.iit.edu>
>> > wrote:
>> >>
>> >> Hi Dan,
>> >>
>> >> Thanks for your response. While I agree that what you've posted
>> *should*
>> >> work as is, it unfortunately does not. The first frame of the
>> trajectory
>> >> is reordered appropriately, but subsequent frames are riddled with
>> strange
>> >> atom configurations: for example, the atoms within C-J get lumped into a
>> >> giant ball instead of being mapped to their original locations. I am
>> not
>> >> too familiar at working with trajectories as COORDS sets, so I can't
>> offer
>> >> a guess as to why this may be occurring.
>> >>
>> >> That being said, my most pressing need is to use cpptraj to identify
>> >> different structural clusters in groups A and B, so I've decided to just
>> >> strip my data to these groups and then use atommap on the resulting
>> >> trajectories prior to clustering. While being able to use a wider
>> variety
>> >> of cpptraj's utilities on the full simulations would be fantastic, this
>> >> will satisfy my original plans for these trajectories.
>> >>
>> >> Thanks again for your assistance.
>> >>
>> >> Take care,
>> >> Samuel Bowerman
>> >> Ph.D. Candidate
>> >> Department of Physics
>> >> Illinois Institute of Technology
>> >>
>> >> On Fri, Aug 26, 2016 at 3:40 PM, Daniel Roe <daniel.r.roe.gmail.com>
>> >> wrote:
>> >>
>> >> > On Tue, Aug 23, 2016 at 3:23 PM, Samuel Bowerman
>> >> > <sbowerma+amber-l.hawk.iit.edu> wrote:
>> >> > >
>> >> > > If I inspect the atommap.dat file, then I get the expected Target
>> <->
>> >> > > Reference index mapping for fragments 1 and 2, but fragments 3
>> through
>> >> > > 10
>> >> > > are filled with "--- ---" for target indices and names. I believe
>> >> > > this
>> >> > > may be a result of those fragments not requiring mapping, but I have
>> >> > > also
>> >> > > found a two-year old thread
>> >> > > (http://archive.ambermd.org/201504/0141.html
>> >> > )
>> >> > > that mentioned system size potentially being an issue - my system is
>> >> > > roughly 30,000 atoms.
>> >> >
>> >> > Oh boy - yeah that's way bigger than any system I've tested 'atommap'
>> >> > on. It was originally developed to re-map small drug-like molecules. I
>> >> > don't remember offhand but I think the largest I ever tested on was
>> >> > about 128 atoms or so. I could probably enhance the performance a lot
>> >> > by doing things on a per-residue basis but there was no real demand
>> >> > for it when I was originally writing the code and unfortunately I
>> >> > haven't had a lot of free time.
>> >> >
>> >> > If the fragments themselves are contiguous and all that has changed is
>> >> > the ordering, i.e. the original is:
>> >> >
>> >> > A B C ...
>> >> >
>> >> > and the new order is
>> >> >
>> >> > B A C ...
>> >> >
>> >> > what you might be able to do is manually reorder whichever trajectory
>> >> > (or trajectories) are shortest via 'strip' and 'combinecrd'. For
>> >> > example, say I wanted to reorder the first to match the second. I
>> >> > would do something like this (I'm oing to use COORDS data sets so I'm
>> >> > assuming you have enough memory):
>> >> >
>> >> > parm All.parm7
>> >> > # Load entire trajectory as COORDS set A
>> >> > loadcrd All.nc name A
>> >> > # Strip everything but A from COORDS set A
>> >> > crdaction A strip !<mask for A>
>> >> > # Repeat for B
>> >> > loadcrd All.nc name B
>> >> > crdaction B strip !<mask for B>
>> >> > # Repeat for C-J
>> >> > loadcrd All.nc name CJ
>> >> > crdaction CJ strip !<mask for C-J>
>> >> > # Combine
>> >> > combinecrd B A CJ crdname Reorder
>> >> > # Write out
>> >> > crdout Reorder Reorder.nc
>> >> >
>> >> > Haven't tested the above but I think it will work. Hope this helps,
>> >> >
>> >> > -Dan
>> >> >
>> >> > >
>> >> > > If anyone could suggest an explanation, a fix, or a work-around for
>> >> > > this
>> >> > > problem, I would greatly appreciate it. Thanks!
>> >> > >
>> >> > > Take care,
>> >> > > Samuel Bowerman
>> >> > > Ph.D. Candidate
>> >> > > Department of Physics
>> >> > > Illinois Institute of Technology
>> >> > > _______________________________________________
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>> >> > > 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 307
>> >> > Salt Lake City, UT 84112-5820
>> >> > http://home.chpc.utah.edu/~cheatham/
>> >> > (801) 587-9652
>> >> > (801) 585-6208 (Fax)
>> >> >
>> >> > _______________________________________________
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>> >> >
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>> >
>> >
>> > --
>> > -------------------------
>> > Daniel R. Roe, PhD
>> > Department of Medicinal Chemistry
>> > University of Utah
>> > 30 South 2000 East, Room 307
>> > Salt Lake City, UT 84112-5820
>> > http://home.chpc.utah.edu/~cheatham/
>> > (801) 587-9652
>> > (801) 585-6208 (Fax)
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe
>> Laboratory of Computational Biology
>> National Institutes of Health, NHLBI
>> 5635 Fishers Ln, Rm T900
>> Rockville MD, 20852
>> https://www.lobos.nih.gov/lcb
>>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Sep 20 2016 - 08:30:04 PDT
