[gmx-users] Deshuffling a .gro file

[toma0052]

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.  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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> 
> 
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