-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Saturday 28 August 2004 05:37, Miguel wrote: > Rajarshi wrote: > > Thanks. I've attached the input file for the gamess run (water.inp), the > > output file (water.dat) as well as stdout (piped to a file, water.out) > > Rajarshi, > > The names file you provided contains the following: > ATOM ATOMIC COORDINATES (BOHR) > CHARGE X Y Z > O 8.0 0.0000000000 0.0000000000 -0.1344644964 > H 1.0 -1.4325701265 0.0000000000 1.0670242942 > H 1.0 1.4325701265 0.0000000000 1.0670242942 > > Q: How is this 'atomic charge' column supposed to be interpreted? Doesn't > look like a 'charge' to me ... looks more like an atomic number ... but it > has a decimal point.
I think that in this case no charge was calculated. I've seen more often where a charge fields gives the total electon density on the atom. If a partial atomic charge was calculated, thess numbers would deviate from the number of electrons the atoms would have in unbounded state. E.g., the O has 8 protons, so in unbounded state, 8 electrons, so that the total charge is zero. When it would have a partial charge, the charge density on the atom would be something like 8.22, while the protons then would be something like 0.89. The 'total' charge is called the Mulliken charge, e.g. HEAD/samples/ch3oh_gam.out, line 377-384. The column right of the Mulliken charge is the charge you should read for partial charge... I think the coordinate section to state are actually input coordinates, but I think the Gammess run for methanol does not do an geometry optimization, so no calculated coordinates are given, but take care with other files... Egon - -- [EMAIL PROTECTED] PhD on Molecular Representation in Chemometrics Radboud University, Nijmegen http://www.cac.science.ru.nl/people/egonw/ GPG: 1024D/D6336BA6 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.4 (GNU/Linux) iD8DBQFBMDIbd9R8I9Yza6YRAj85AJ9lgTKsAXzBWAVPZc69vJ7hEEj4QwCfa0D8 6G3sUVGX4GRJfpeXfRzsx2g= =rWIv -----END PGP SIGNATURE----- ------------------------------------------------------- This SF.Net email is sponsored by BEA Weblogic Workshop FREE Java Enterprise J2EE developer tools! Get your free copy of BEA WebLogic Workshop 8.1 today. http://ads.osdn.com/?ad_idP47&alloc_id808&op=click _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
