[gmx-users] editconf not centering, and it is cutting off my molecule

[Justin Lemkul]

On 12/31/12 5:40 PM, Xu Dong Huang wrote:
> Dear Justin,
>
> (here is the picture of the molecule after editconf, note the negative x and negative y axis is missing the rest of the beads that is suppose to be like the positive x and positive y)
> http://i1284.photobucket.com/albums/a571/X_huang1/ScreenShot2012-12-31at53618PM_zpse5f421f1.png
>
> *Even though according to the .gro coordinates, those beads of 175 and up are jumped, i don't see the relocated beads anyhow in this VMD viewing. I'm so confused of what is happening.
>

Is your .gro file valid?  Specifically, does the second line of the input file 
specify the correct number of atoms?  Does the output file have the same number 
of atoms as the input?  That is the only reason I know of for a file being 
truncated.

-Justin

>
> Xu Dong Huang
> Chemical & Biochemical Engineering
> Rutgers School of Engineering
> xudongh at eden.rutgers.edu
>
> On Dec 31, 2012, at 5:31 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 12/31/12 4:53 PM, Xu Dong Huang wrote:
>>> Dear advanced gromacs users,
>>>
>>> I have created an arbitrary molecule .gro file containing coordinates of my martini-beads. basically, there are 50 beads sitting on each axis of (x,y, -x and -y) forming like a cross. (Each bead with distance 0.43). However, when I try to use editconf on my .gro file to generate a box (editconf -f star.gro -o star_box.gro -c -d 1.0 -bt cubic) , it gives me back a new .gro file with a bad molecule. In VMD viewing, I see that the negative axis part of my molecules are cut off. Closer inspection shows the following for a particular segment of the molecule coordinates:
>>>
>>> **original .gro coordinates:
>>>      1star     O1     170   0.000  -8.170   0.000
>>>      1star     O1     171   0.000  -8.600   0.000
>>>      2star     O2     172   0.000  -9.030   0.000
>>>      2star     O2     173   0.000  -9.460   0.000
>>>      2star     O2     174   0.000  -9.890   0.000
>>>      2star     O2     175   0.000 -10.320   0.000
>>>      2star     O2     176   0.000 -10.750   0.000
>>>      2star     O2     177   0.000 -11.180   0.000
>>>      2star     O2     178   0.000 -11.610   0.000
>>>      2star     O2     179   0.000 -12.040   0.000
>>>      2star     O2     180   0.000 -12.470   0.000
>>>      2star     O2     181   0.000 -12.900   0.000
>>>      2star     O2     182   0.000 -13.330   0.000
>>>      2star     O2     183   0.000 -13.760   0.000
>>> *new .gro coordinates:
>>>
>>> 1star      O1      169  12.421   4.681  16.695
>>>      1star      O1      170  12.421   4.251  16.695
>>>      1star      O1      171  12.421   3.821  16.695
>>>      2star      O2      172  12.421   3.391  16.695
>>>      2star      O2      173  12.421   2.961  16.695
>>>      2star      O2      174  12.421   2.531  16.695
>>>      2star      O2      175  12.421  22.741  16.695
>>>      2star      O2      176  12.421  23.171  16.695
>>>      2star      O2      177  12.421  23.601  16.695
>>>      2star      O2      178  12.421  24.031  16.695
>>>      2star      O2      179  12.421  24.461  16.695
>>>      2star      O2      180  12.421  24.891  16.695
>>>      2star      O2      181  12.421  25.321  16.695
>>>      2star      O2      182  12.421  25.751  16.695
>>>      2star      O2      183  12.421  26.181  16.695
>>>
>>> Notice the jump on atom number 174 and 175, why is there a sudden coordinate jump?
>>> All i can see in VMD is my negative axis part of the molecule beads are cut off.
>>>
>>
>> editconf builds boxes from the coordinate origin so that there are never negative coordinates.  It should be able to deal with those coordinates, equally shifted, which it appears they were.  Can you provide images of what's going on?  I don't clearly understand what's wrong.  What do you mean by "cut off?" Nonexistent?  Incorrectly placed?
>>
>> -Justin
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> 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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-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================