Files::PTS: Difference between revisions

From FFDevel Wiki
Jump to navigation Jump to search
No edit summary
No edit summary
Line 25: Line 25:
| definition of electrostatic potential. The next line contains number of ESP points, followed by ESP points. Each ESP point has x, y, and z coordinate in Å and value of ESP (not yet determined).
| definition of electrostatic potential. The next line contains number of ESP points, followed by ESP points. Each ESP point has x, y, and z coordinate in Å and value of ESP (not yet determined).
|}
|}
==Example==
<pre>
14
extracted from gaussian
6      0.13230016      0.00000077      -1.95468488
1      0.76809047      0.88672039      -2.09551250
1      -0.62227433      0.00000027      -2.75333837
1      0.76809127      -0.88671834      -2.09551220
6      -0.51108991      0.00000067      -0.56887531
1      -1.16736722      -0.88018194      -0.46376311
1      -1.16736732      0.88018319      -0.46376304
6      0.51109004      0.00000067      0.56887531
1      1.16736736      -0.88018195      0.46376311
1      1.16736747      0.88018319      0.46376303
6      -0.13230001      0.00000077      1.95468489
1      -0.76809113      -0.88671834      2.09551220
1      0.62227447      0.00000027      2.75333837
1      -0.76809032      0.88672039      2.09551250
ENERGY
-99324.33757012
GRADIENT
      0.11579154      0.00000710      -0.16491661
    -0.03290464      -0.03371546      0.03452853
      0.00516174      -0.00000388      0.07031637
    -0.03290310      0.03371450      0.03453062
    -0.20334654      0.00000002      0.17824297
      0.03625131      0.05934802      -0.03143532
      0.03625573      -0.05935031      -0.03143510
      0.20334573      0.00000003      -0.17824440
    -0.03625143      0.05934780      0.03143565
    -0.03625584      -0.05935008      0.03143544
    -0.11578914      0.00000710      0.16491851
      0.03290314      0.03371407      -0.03453083
    -0.00516318      -0.00000389      -0.07031707
      0.03290468      -0.03371502      -0.03452875
</pre>

Revision as of 13:42, 4 March 2019

Point file specification.

A point file is an extended xyz file. Coordinates are in Å. Extensions are attached as named sections after coordinate specification.

Section Description
ENERGY Energy in kcal/mol is provided on the next line.
GRADIENT Gradient is provided in kcal/mol/Å in three columns starting from the next line.
HESSIAN Hessian is provided in kcal/mol/Å^2 as the full square matrix.
WEIGHT weight of the point
CVS definition of collective variables for geometry restraining. The next line contains number of CVs. Description of each CV then follows.
ESP definition of electrostatic potential. The next line contains number of ESP points, followed by ESP points. Each ESP point has x, y, and z coordinate in Å and value of ESP (not yet determined).

Example

14
extracted from gaussian
 6       0.13230016       0.00000077      -1.95468488
 1       0.76809047       0.88672039      -2.09551250
 1      -0.62227433       0.00000027      -2.75333837
 1       0.76809127      -0.88671834      -2.09551220
 6      -0.51108991       0.00000067      -0.56887531
 1      -1.16736722      -0.88018194      -0.46376311
 1      -1.16736732       0.88018319      -0.46376304
 6       0.51109004       0.00000067       0.56887531
 1       1.16736736      -0.88018195       0.46376311
 1       1.16736747       0.88018319       0.46376303
 6      -0.13230001       0.00000077       1.95468489
 1      -0.76809113      -0.88671834       2.09551220
 1       0.62227447       0.00000027       2.75333837
 1      -0.76809032       0.88672039       2.09551250
ENERGY
 -99324.33757012
GRADIENT
      0.11579154       0.00000710      -0.16491661
     -0.03290464      -0.03371546       0.03452853
      0.00516174      -0.00000388       0.07031637
     -0.03290310       0.03371450       0.03453062
     -0.20334654       0.00000002       0.17824297
      0.03625131       0.05934802      -0.03143532
      0.03625573      -0.05935031      -0.03143510
      0.20334573       0.00000003      -0.17824440
     -0.03625143       0.05934780       0.03143565
     -0.03625584      -0.05935008       0.03143544
     -0.11578914       0.00000710       0.16491851
      0.03290314       0.03371407      -0.03453083
     -0.00516318      -0.00000389      -0.07031707
      0.03290468      -0.03371502      -0.03452875