VMD-L Mailing List

From: Jennifer Williams (Jennifer.Williams_at_ed.ac.uk)
Date: Wed Dec 09 2009 - 06:39:48 CST

Quoting Olaf Lenz <lenzo_at_mpip-mainz.mpg.de>:

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> Hi!
>
> Olaf Lenz wrote:
>> Axel Kohlmeyer wrote:
>>> before investing much effort, try if using
>>> ::TopoTools::replicatemol does the trick for this.
>>> arguments are "molid nx ny nz", i.e. top 2 2 2
>>> will replicate the molecule twice in each direction.
>
> Unfortunately, ::TopoTools::replicatemol apparently can not
> handle non-orthorhombic boxes, which is crucial for the problem at hand...
>
> Olaf
> - --

HI Axel, Olaf,

Thanks for your suggestions-I managed to get around the problem as my
trajectory was created in gromacs so I used gromacs to make the box a
2x2x2 unit cell. In case anyone else has the same problem:

I made the structure file bigger using:

genconf -nbox 2 2 2 -f confout.gro -o confbig.out

2. Convert traj.xtc to single frames:

trjconv -s md.tpr -sep -nzero 0 -f traj.xtc -o fr.gro

Use genconf on each of these frames as above (I wrote a script to do
this for all frames)

3. Stick the new, bigger frames into a trajectory using trjcat

I had to split the trajectory into single frames as I don't have a
cubic box. I think you could use the -box option with trjconv if you
had a cubic box,

I'd still be interested to hear of any VMD solutions to this problem
but its not urgent from my point of view,

Thanks again

Jenny

qsub MULTIPLY.sh 

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