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Pallavi-Banerjee21 / votca

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dlpoly topology reader (c++ part) does read bonds, angle and exclusion #147

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
Without bonds, exclusion etc., some distribution functions might be calculated 
incorrectly (too many pairs).

As a workaround until this is implemented one can create a xml topolgy file on 
top of the dlpoly topology.

Original issue reported on code.google.com by christop...@gmail.com on 11 Nov 2013 at 9:32

GoogleCodeExporter commented 8 years ago 
Seems to me as a good option for workaround. What is missing for bonded
interactions?

sorry for typos, if any - sent from my Andreid mobile

Original comment by abruk...@googlemail.com on 11 Nov 2013 at 10:23

GoogleCodeExporter commented 8 years ago 
How does dl_poly generate exclusions? Only from the bonds, angles and dihedrals 
directive in MOLECULES block or are there other ways, too?

Original comment by christop...@gmail.com on 12 Nov 2013 at 12:13

GoogleCodeExporter commented 8 years ago 
Gromacs has a variable, which defines how many "bonds" away an atom is 
excluded. Does dlpoly have something similar?

Original comment by christop...@gmail.com on 12 Nov 2013 at 4:18

GoogleCodeExporter commented 8 years ago

Original comment by christop...@gmail.com on 12 Nov 2013 at 8:40

GoogleCodeExporter commented 8 years ago 
This issue was updated by revision a13b5f11e021.

Original comment by christop...@gmail.com on 17 Nov 2013 at 12:36

GoogleCodeExporter commented 8 years ago 
Exclusions are now implemented in the C++ dlpolytopology reader.

Original comment by christop...@gmail.com on 17 Nov 2013 at 8:16

GoogleCodeExporter commented 8 years ago 
Fortran layer got removed, so this is fixed.

Original comment by christop...@gmail.com on 18 Nov 2013 at 4:13