[gmx-users] box vectors

[Matthew Zwier]

Impressive :)

On Wed, Dec 7, 2011 at 1:34 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> #!/usr/bin/env python
>
> # Python compliant email -- Just save the content :)
>
>
> """
>
> Hey :)
>
> The neatest way is using python to extract them from the XTC file :)
>
> """
>
> from struct   import unpack
> import sys
> import os
>
> def i(x): return sum([ord(x[j])<<(24-j*8) for j in range(4)])
>
> def strseek(stream,s,bufsize=10000):
>    v = len(s)
>    x = stream.read(bufsize)
>    n = 0
>    while len(x) >= v:
>        m = x.find(s)
>        if m > -1:
>            # If we found the tag, the position is the total length
>            # read plus the index at which the tag was found
>            n += m
>            yield n
>            # Now we strip the part up to and including the tag
>            x = x[m+v:]
>            n += v
>        elif len(x) > v:
>            # If the tag was not found, strip the string, keeping only
>            # the last v-1 characters, as these could combine with the
>            # next part to be read in.
>            # n is incremented with the number of characters taken from
>            # the current string x (len(x)-v+1)
>            n += len(x)-v+1
>            x = x[1-v:]
>        if len(x) <= v:
>            x += stream.read(bufsize)
>
> # Get the tag to identify the start of a frame
> f   = open(sys.argv[1])
> tag = f.read(8)                     # Tag: magic number and number of atoms
> n   = 92 + i(f.read(84)[-4:])       # Size of frame in bytes
> f.close()
>
> # Find all positions at which the tag is found and the frame lengths
> frames  = [ i for i in strseek(open(sys.argv[1]),tag) ]
> nf      = len(frames)
> lengths = [ j-i for i,j in zip(frames,frames[1:]+[nf]) ]
> f       = open(sys.argv[1])
> print (10*"%10s")%("Time","XX","XY","XZ","YX","YY","YZ","ZX","ZY","ZZ")
> for i in frames:
>    print (10*" %10.5f")%(f.seek(i) or unpack(">ffffffffff",f.read(52)[-40:]))
>
> """
> Cheers,
>
> Tsjerk
> """
>
> """
>
> On Wed, Dec 7, 2011 at 7:29 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> Chandan Choudhury wrote:
>>>
>>>
>>> Dear gmx_users,
>>>
>>> I am using gmx_4.0.7. I need to print the box vectors from the trajectory
>>> of a simulated system. How can this be achieved? Can someone help me out?
>>>
>>
>> Box vectors are stored in the .edr file.
>>
>> -Justin
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> --
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
>
> """
> --
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