[gmx-users] Deshuffling a .gro file

[Yang Ye]

toma0052 wrote:
> Hi,
>      Thanks for the response.  Sorry that the statement of my problem was so
> cumbersome.  My problem was with the noncontinuous numbering of molecules
> following deshuffling using editconf.  What I am doing, is following an md
> run, performing a simple transformation of the coordinates in the resulting
> *.gro file (to simulate a stretch, and then relaxation of a lipid bilayer). 
> The noncontinuous numbering of the molecules following deshuffling makes this
> transformation much harder.  Therefore, I was hoping to get a *.gro file
> which has the correct numbering following deshuffling.  
The numbering of the solvent water doesn't have a rule, e.g. water X and 
Y could be just neighbour even X=1000 and Y=10000. It only depends on 
the initial ordering imposed by the stacking algorithm of genbox. During 
the course of MD, every molecule drifts especially the solvents and ions 
so the number ordering is no longer an indicator; actually, it is always 
not an good indicator for anything. So your intention about using such 
numbering sounds not reasonable. You shall always sort your molecules 
based on their coordinates.
> However, it appears
> that deshuffling and sorting the atoms in a *.gro file is quite nontrivial,
> so now I have taken to not running my simulation in parallel, or not using
> the -shuffle -sort option and just dealing with the longer run times.  Thanks
> for the advice.
>
> Mike    
>
>
>
> On 27 Mar 2007, Yang Ye wrote:
>   
>> On 3/20/2007 10:03 PM, toma0052 wrote:
>>     
>>> Hello,
>>>      I am performing a simulation in parallel on four processors.  The
>>> simulation seems to run fine, and outputs a shuffled *.gro file.  I would
>>> like to change the order of atoms to what they were in the original input
>>> *.gro file, but I am having some trouble.  I have seen some previous
>>>       
> posts
>   
>>> on this, but I am still a bit confused. 
>>>
>>> David van der Spoel wrote:
>>>   
>>> [...]
>>>
>>>   
>>>       
>>>> If your standard dsehuf.ndx for a system of N atoms starts with:
>>>> [ deshuf ]
>>>> 0 1 4 6 7 etc.
>>>> you have to modify it to the old format:
>>>> 1 N
>>>> deshuf N
>>>> 0 1 4 6 7 etc.
>>>>
>>>> You only have to change the top bit, not the actual numbers. An
>>>> alternative is to modify it to be:
>>>> [ deshuf ]
>>>> 1 2 5 7 8 etc.
>>>>
>>>> That wouldn't be too hard with a script either.
>>>>
>>>>     
>>>>         
>>> This says that I need to alter my deshuf.ndx file a bit, and then just do
>>> editconf -f shuf.gro -n deshuf.ndx -o unshuf.gro  to obtain an unchuffled
>>> *.gro file.  However, my deshuf.ndx file already began counting the atoms
>>> at 1, i.e.:
>>>
>>> [ DeShuffle ]
>>>   1  2  3  4  5  6  7  8  9  10
>>>   11  12  13  14  15  16  17  18  19  20
>>>   21  22  23  24  25  26  27  28  29  30
>>>   31  32  33  34  35  36  37  38  39  40
>>>   41  42  43  44  45  46  47  48  49  50
>>> ...
>>>
>>> So, everything already seems to be fine (other than the name in the
>>> brackets, which didn't seem to matter if changed) with the deshuf.ndx
>>>       
> file.
>   
>>>  When I do editconf -f shuf.gro -n deshuf.ndx -o unshuf.gro  though, my
>>> *.gro file does not sort properly, although some sorting does take place.
>>>       
>
>   
>>> The atoms seem to be in the correct general order (The first series of
>>> atoms are all DPPC, and the rest are all SOL) but the atom numbers are in
>>> the wrong order (The order goes 1DPPC ... 44DPPC, 1257DPPC ... 1299DPPC,
>>> 2513DPPC ... etc whereas it should go from 1DPPC to 128DPPC and then
>>>       
> begin
>   
>>> to number the SOL molecules at 129SOL).  Is this a problem with my input
>>> into grompp?  I am using both -shuffle and -sort.  Is this incorrect?
>>> How do I deshuffle my *.gro file to list the 128 DPPC molecules and then
>>> the 3655 SOL molecules with atom numbers 1 to 17365?
>>>   
>>>       
>> Sorry that your description was not easy to be comprehend. Perhaps this 
>> is why this post was not followed.
>> I would like to offer some general principles here.
>> 1. deshuf.ndx is definitely not ordered so you shall see some 
>> disordering in the later part of ndx file.
>> 2. After deshuffling using editconf, it is normal for the resulting .gro 
>> to have noncontinuous numbering for molecule. It is more important to 
>> have the correct molecule type. For example, all your SOL shall be in 
>> one block with no other molecules embedded.
>>
>>
>> Yang Ye
>>     
>>> Thank you,
>>> Mike Tomasini
>>>
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