NEEMP:Getting started: Difference between revisions

Revision as of 10:57, 21 June 2016

NEEMP's binary file is available online (http://ncbr.muni.cz/NEEMP) together with the examples.tar.bz2 file containing all the input files needed to run the examples and get acquainted with the tool. These files include:

set01.sdf -- 500 molecules (H, C, N, O, S), records in MOL V2000

set02.sdf -- 500 molecules (H, C, N, O, S), records in MOL V2000

set03.sdf -- 500 molecules (H, C, N, O, S), records in MOL V3000

charges.chg -- Reference QM charges for all molecules in set01, set02 and set03. Theory level, basis set and population analysis: HF/6-31GH/Mulliken

Element.par -- parameters calculated using set03 for atom types determined by element only

ElemBond.par -- parameters calculated using set03 for atom types determined by element + maximum bond order

NEEMP can then be run simply by calling the command ./neemp. For instance, to get information about basic usage, use:

~/neemp/$ ./neemp --help

Click on the link to see the complete options list.

@@ Line 1: / Line 1: @@
-<span style="color:#FF0000"> waiting for instructions on how to retrieve the executable file </span>
+'''NEEMP''''s binary file is available online ([http://www.fi.muni.cz/~xracek/neemp/ http://ncbr.muni.cz/NEEMP]) together with the ''examples.tar.bz2'' file containing all the input files needed to run the [[NEEMP:Examples | examples]] and get acquainted with the tool. These files include:
+* '''set01.sdf''' -- 500 molecules (H, C, N, O, S), records in MOL V2000
+* '''set02.sdf''' -- 500 molecules (H, C, N, O, S), records in MOL V2000
+* '''set03.sdf''' -- 500 molecules (H, C, N, O, S), records in MOL V3000
+* '''charges.chg''' -- Reference QM charges for all molecules in set01, set02 and set03. Theory level, basis set and population analysis: HF/6-31GH/Mulliken
+* '''Element.par''' -- parameters calculated using set03 for atom types determined by element only
+* '''ElemBond.par''' -- parameters calculated using set03 for atom types determined by element + maximum bond order
 '''NEEMP''' can then be run simply by calling the command <code>./neemp</code>. For instance, to get information about basic usage, use:
@@ Line 6: / Line 18: @@
 Click on the link to see the complete [[NEEMP:Options | options list]].
-Before proceeding in the description of '''NEEMP''''s modes, here we introduce a tree representation of '''NEEMP''''s main directory to assist the user in the examples understanding.
-'''NB:''' the ''examples'' directory contains all the files employed in the [[NEEMP:examples]] section. ''src'' directory has not been expanded to improve the readability.
- <nowiki>
-/neemp
-├── examples
-│   ├── charges.chg
-│   ├── ElemBond.par
-│   ├── Element.par
-│   ├── NOTES
-│   ├── set01.sdf
-│   ├── set02.sdf
-│   └── set03.sdf
-├── LICENCE
-├── Makefile
-├── misc
-│   ├── template
-│   ├── valgrind-suppresions
-│   └── web-update.sh
-├── README
-└── src
-</nowiki>