VMD-L Mailing List

From: Mgr. Lubos Vrbka (lubos.vrbka_at_uochb.cas.cz)
Date: Sat May 20 2006 - 04:24:10 CDT

dear john,

> The FIELD file contains "molecules" which other programs might consider
> to be chains. It's conceivable we could parse those FIELD molecules and treat
> them as chains/segnames in VMD. The main problem I see with that is that
> I didn't see anything in the DLPOLY documentation that relates the atom indices
> of the CONFIG/HISTORY files with the atoms in the FIELD file, particularly
> those that are in different "molecules" in the FIELD file. Any tips?
i hope i got your question right - so here comes my explanation:

the FIELD file serves as a topology/parameter file. in the beginning you
define the number of distinct 'molecules' - atoms / ions / molecules -
whatever you want to treat as a separate entity.

then, for each 'molecule' you specify the number of these in your
structure and also its constituents (i.e., single atom / ion /
collection of atoms forming e.g. water molecules, ...). you also specify
 the topology - core-shell, angles, bonds, etc. with their parameters there.

at the end of the file, you specify all nonbonded interaction parameters.

the CONFIG file has to contain the names/coordinates of the respective
particles in the same arrangement/order as in your FIELD file, otherwise
you get an error. there was lately a change introduced to FIELD file
(change from fixed format to free format and some minor changes, but
with respect to visualization, these things shouldn't affect anything).

relatively simple example for zeolite plus water + ion (old dlpoly
format - up to version 2.14):

*********************************************************
Sample FIELD for zeolite with Nachtigall et al. water model
units eV
molecules 7
zeolite framework silicon
nummols 142
atoms 1
 Si 28.0860 4.0000 1
finish
zeolite framework aluminium
nummols 2
atoms 1
 Al 26.9820 3.0000 1
finish
zeolite framework oxygen
nummols 288
atoms 2
 O 15.8000 1.22858 1
 Os 0.2000 -3.22858 1
shell 1
    1 2 122.47853
finish
extraframework Na(+)
nummols 0
atoms 1
 Na 22.9900 1.0000 1
finish
extraframework Cu(+)
nummols 0
atoms 1
 Cu 63.5500 1.0000 1
finish
extraframework Cu(2+)
nummols 1
atoms 1
 Cu2 63.5500 2.0000 1
finish
water molecule
nummols 36
atoms 4
 OW 15.8000 0.88775 1
 OWs 0.2000 -2.88775 1
 HW 1.0000 1.00000 2
shell 1
    1 2 77.992681
bonds 4
-bck 2 3 -92.9371 0.371252 0.00000000
-bck 2 4 -92.9371 0.371252 0.00000000
-bck 2 3 327.3590 0.238060 0.00000000
-bck 2 4 327.3590 0.238060 0.00000000
finish
vdw 13
 Si Os buck 1612.45920 0.299550 0.0000000
 Al Os buck 1395.77463 0.304490 0.0000000
 Na Os buck 5836.84000 0.238700 0.0000000
 Cu Os buck 2676.72719 0.242430 0.0000000
 Cu2 Os buck 712.80000 0.327000 0.0000000
 Si OWs buck 480.96671 0.386113 0.0000000
 Al OWs buck 574.97398 0.343311 0.0000000
 Os OWs buck 14274.03000 0.227930 0.0000000
 Os HW buck 1089.22570 0.232753 0.0000000
 Na OWs buck 796.091759 0.323653 0.0000000
 Cu OWs buck 2676.72719 0.242430 0.0000000
 Cu2 OWs buck 543.40084 0.369432 0.0000000
 OWs HW buck 92.93710 0.371252 0.0000000
tbp 2
 Os Si Os shrm 0.144703 109.47 1.0e+5
1.0e+5 2.00000
 Os Al Os shrm 0.893930 109.47 1.0e+5
1.0e+5 2.00000
close
*********************************************************

according to this field file, the CONFIG will consist of
header
coordinates of 142 Si atoms
coordinates of 2 Al atoms
coordinates of 288 O 'atoms'
        each consists of core and shell 'subparticle'
no coordinates of Na, Cu ions
coordinate of 1 Cu(2+) ion
coordinates of 36 water molecules
        OW oxygen core
        OWs oxygen shell
        HW hydrogen
        HW hydrogen

if required, the file also contains velocities and forces.
the same applies to HISTORY file.

so you can directly relate the FIELD with the CONFIG/HISTORY - you just
assign the atomic indices as you pass the FIELD and you can use them for
CONFIG/HISTORY.

i hope this can be of some help for you. if you have more questions
please let me know.

regards,
lubos 

-- 
.....................................................
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
.....................................................