Re: [AMBER] fix_traj_parm.py problems

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 12 Jul 2013 00:26:03 -0400

Perhaps it is more inefficient than I thought. Just one frame of my 200K atom test took a VERY long time to finish I will try to find out why (I'm probably doing something stupid). In fact, my first attempt to reorder the atoms in the prmtop resulted in an algorithm that took 45 minutes in Python on a 100K atom system (the current one takes about a second).

I have some ideas to try out. 

--
Jason Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
--
Jason Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Jul 11, 2013, at 11:33 PM, Jason Swails <jason.swails.gmail.com> wrote:
> 
> 
> On Jul 11, 2013, at 11:18 PM, Fabrício Bracht <fabracht1.gmail.com> wrote:
> 
>> Hi Jason. Thank you for the update. When you said that is going to be quite
>> slow, did you mean that it would take days. Cause I've been running it for
>> about 4 hours and the
>> Re-ordering the trajectories. This may take awhile...
>> Adding mdcrd.md2: 0%
>> Is still at 0%. The system has less than 30k atoms and the simulation has
>> 10k frames.
>> Is this what I should expect?
>> Thanks
> 
> Ugh. I don't think it should take that long. It worked fine in my tests, but that was admittedly a small test without periodic boundaries. I will look into it when I get some time. 
> 
> Is this a set of simulations that would be easy to rerun with a fixed topology file and restart file? Because ParmEd will fix this prmtop and restart for you. 
> 
> Also, cpptraj will now work on these broken prmtops for any action that doesn't require molecule information, so you may be able to get away without reordering the trajectories. 
> 
> In the meantime, it may be a good idea to check the validity of your prmtop using the checkValidity command in parmed before running simulations to check that everything looks good. As a plus side, it will catch numerous other errors, like forgotten disulfide bridges and other issues. 
> 
> HTH,
> Jason
> 
> 
>> 
>> 
>> 2013/7/11 Jason Swails <jason.swails.gmail.com>
>> 
>>> On Thu, Jul 11, 2013 at 7:04 PM, Fabrício Bracht <fabracht1.gmail.com
>>>> wrote:
>>> 
>>>> Hi Jason. Indeed my input had a silly mistake. Instead of using -x to
>>>> indicate the output trajectory, I used -y again. Very silly indeed.
>>>> Now I have another error.
>>>> The input line
>>>> ./fix_traj_parm.py -p HOH_wat.prmtop -y mdcrd.md2 mdcrd.md3 -o
>>>> fixedparm.prmtop -x fixed.mdcrd
>>>> seems to be correct, but an error comes up anyway:
>>>> 
>>>> Re-ordering the trajectories. This may take awhile...
>>>> Traceback (most recent call last):
>>>> File "./fix_traj_parm.py", line 110, in <module>
>>>>   pbcang =
>>>> newtraj.createVariable('cell_angular','d',('frame','cell_angular'))
>>>> IOError: netcdf: NetCDF: String match to name in use
>>>> 
>>> 
>>> Ah, a stupid typo (in 2 places, actually).
>>> 
>>> When I tested this script, I created an system without PBC, so I never
>>> tested this particular bit of code...  It seems to work now, although it
>>> may be quite slow for large systems (it is in Python, after all).
>>> 
>>> I've uploaded the fixed version to my Wiki.
>>> 
>>> Thanks,
>>> Jason
>>> 
>>> 
>>>> I have tried with two different sets of trajectories and the error was
>>> the
>>>> same.
>>>> 
>>>> 
>>>> 
>>>> 2013/7/11 Jason Swails <jason.swails.gmail.com>
>>>> 
>>>>> On Thu, Jul 11, 2013 at 1:30 PM, Fabrício Bracht <fabracht1.gmail.com
>>>>>> wrote:
>>>>> 
>>>>>> Hi Jason. Thanks for the reply. It worked fine until it started
>>> working
>>>>> on
>>>>>> the trajectory. Here is the screen output:
>>>>>> 
>>>>>> Re-ordering the trajectories. This may take awhile...
>>>>>> Traceback (most recent call last):
>>>>>> File "./fix_traj_parm.py", line 70, in <module>
>>>>>>   newtraj = open_netcdf(opt.outtraj, 'w')
>>>>>> File "/home/fabricio/amber12/bin/chemistry/amber/readparm.py", line
>>>> 45,
>>>>>> in <lambda>
>>>>>>   open_netcdf = lambda name, mode: NetCDFFile(name, mode)
>>>>>> File "/usr/lib/python2.7/dist-packages/Scientific/IO/NetCDF.py",
>>> line
>>>>>> 171, in NetCDFFile
>>>>>>   filename = os.path.expanduser(filename)
>>>>>> File "/usr/lib/python2.7/posixpath.py", line 252, in expanduser
>>>>>>   if not path.startswith('~'):
>>>>>> AttributeError: 'NoneType' object has no attribute 'startswith'
>>>>>> 
>>>>>> Looked it up on the web to see if there was something I could do, but
>>>>> found
>>>>>> lots of generic forums discussing things that I didn't really
>>>> understand.
>>>>>> 
>>>>>> Am I missing something here?
>>>>>> 
>>>>> 
>>>>> Could be.  What command-line did you use (user input is frequently
>>>> helpful
>>>>> debugging information)?  It *looks* like you didn't specify an output
>>>>> trajectory on the command-line, so the default "None" (Python
>>> equivalent
>>>> of
>>>>> NULL) was passed to the NetCDF constructor.  Apparently I did not add
>>>> much
>>>>> error checking to make sure that the user input was sufficient.  You
>>> can
>>>>> use the "--help" flag to provide some level of help.
>>>>> 
>>>>> Note, this script does _not_ modify the trajectories in-place.  It
>>>> writes a
>>>>> new trajectory that is a concatenation of all input trajectories (and
>>> so
>>>>> requires you to supply an output trajectory).
>>>>> 
>>>>> This script is intended to be used *once* for your system.  That is, if
>>>> you
>>>>> ran your simulation in 20 chunks, you should supply your prmtop file
>>> and
>>>> 20
>>>>> NetCDF trajectories, after which fix_parm_traj.py will create one new,
>>>>> fixed prmtop and ONE, concatenated, properly ordered NetCDF trajectory.
>>>>> 
>>>>> Hope this helps,
>>>>> Jason
>>>>> 
>>>>> P.S. While 99.9% of my Python scripts have a sophisticated command-line
>>>>> parser that documents all options with the "--help" flag, mature input
>>>>> error-checking I tend to reserve for scripts and programs I release for
>>>>> general use (e.g., MMPBSA.py, ParmEd, cpinutil.py, update_amber, etc.)
>>>>> 
>>>>> --
>>>>> 
>>>>> 
>>>>> Ja
>>>>> 
>>>>> son M. Swails
>>>>> Qu
>>>>> 
>>>>> 
>>>>> antum Theory Project,
>>>>> Un
>>>>> 
>>>>> iversity of Florida
>>>>> Ph.D. Candidate
>>>>> 352-392-4032
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>> 
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>>> 
>>> 
>>> --
>>> Jason M. Swails
>>> Quantum Theory Project,
>>> University of Florida
>>> Ph.D. Candidate
>>> 352-392-4032
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>> 
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> 
> --
> Jason Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Thu Jul 11 2013 - 21:30:06 PDT
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