From: Mgr. Lubos Vrbka (lubos.vrbka_at_uochb.cas.cz)
Date: Thu Jan 19 2006 - 01:58:15 CST

hi john & others,

thanks for the reply.
> I'd suggest having a look at the way the Solvate plugin works, as it
> generates a solvent box by copying a template structure filling the required
> space in much the same manner you'd like to replicate your periodic cell
> into the other 26 neighboring locations. Solvate does this by building
> structures with a combination of atom selections and psfgen. You can
> basically replicate what solvate does and tune it for your particular needs.
i checked the solvate.tcl (i have version 1.2), however still don't
fully understand how it works.

i think the part relevant for me starts around line 176 (it is a comment
- read combined structure back). i don't need to load anything more
since everything (the whole simulation box) is already loaded. however,
i have a suspicion that i'll need the psf file for some reason - and i
don't have it, this is a gromacs trajectory.

then, the translation vector is created and all water molecules are
shifted at the same time. this is clear.

the next part (create a copy of the water molecule) is a mystery to me -
probably because i never worked with psfgen, since these commands seem
to be psfgen-related. it looks like (please correct me if i am wrong):
1) segment is one of the copies of the water box
2) place 'holder' for appropriate number of residues to this segment
(foreach cycle and residue command)
3) enlarge the seglist variable (is it psfgen variable?)
4) cycle through all the original residues and set the properties of the
'holders' in the segment (i.e. coordinates with command coord)

deleting the overlaping molecules doesn't apply in my case. then, moving
the original coordinates back to their initial position - again, clear
here...

the solvate plugin copies all residues. i might do the same thing, but
copying set of individual atoms (only OW, "HW.") might work as well. i'd
first create the appropriate selection
set wat [atomselect top "name OW \"HW.\""]
but how to treat then the part of the code with segment?

after this is worked out, i presume i just need to modify my atomselect
commands like
set sel [ atomselect top "segid $seglist ..... "]
to treate all the replicas. is this true?

also (since i won't need the replicas after the analysis is done, how
can i safely delete all created segments?

=====

isn't there any (easier) route to this problem? re-imaging structure
sequentially for every water doesn't seem to be the correct approach.
how does it look like with the pbc support in measure and other
commands? aren't there currently any workarounds?

thank you for your support and help. with best regards,
lubos

-- 
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Mgr. Lubos Vrbka
Center for Biomolecules and Complex Molecular Systems
Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic
Prague, Czech Republic
http://www.molecular.cz/~vrbka
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