[gmx-users] Deshuffling a .gro file

[Yang Ye]

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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