Files::PTS: Difference between revisions

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Navigation: [[Documentation]] / [[Files]] / [[File Formats]] / [[Files::PTS]]
Navigation: [[Documentation]] / [[Files]] / [[File Formats]] / [[Files::PTS]]
----
----
A PTS file format defines geometry and associated properties. The PTS file is an extended xyz file. All coordinates are in Å. Extensions are attached as named sections after coordinate specification. It is possible to put several points  
A PTS file format defines geometry and associated properties. The PTS file is an extended xyz file. All coordinates are in Å. Extensions are attached as named sections after coordinate specification. Order of sections is free. It is possible to put several points into a single file and to form a stream of points. In this case, all sections must be supported by ffdevel.  
into a single file and to form a stream of points. In this case, all sections must be supported by ffdevel.  


{|class="wikitable"
{|class="wikitable"
Line 26: Line 25:
| ESP
| 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).
| 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).
|}
==Collective variables==
Each CV has order index, followed by a CV type, and target value of CV. The list of currently supported CVs is provided in the following table:
{|class="wikitable"
| '''Type'''
| '''Value unit'''
| '''Description'''
|-
| B
| Å
| distance between two atoms specified by two atom indexes
|-
| A
| deg
| angle between three atoms specified by three atom indexes
|-
| D
| deg
| dihedral angle between four points specified by four atom indexes
|}
|}


Line 64: Line 84:
       0.03290468      -0.03371502      -0.03452875
       0.03290468      -0.03371502      -0.03452875
CVS
CVS
1
2
1 D  169.9998  5  8 11 13
1 D  169.9998  5  8 11 13
2 B    1.3456  5 11
</pre>
</pre>

Revision as of 13:56, 4 March 2019

Navigation: Documentation / Files / File Formats / Files::PTS

A PTS file format defines geometry and associated properties. The PTS file is an extended xyz file. All coordinates are in Å. Extensions are attached as named sections after coordinate specification. Order of sections is free. It is possible to put several points into a single file and to form a stream of points. In this case, all sections must be supported by ffdevel.

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).

Collective variables

Each CV has order index, followed by a CV type, and target value of CV. The list of currently supported CVs is provided in the following table:

Type Value unit Description
B Å distance between two atoms specified by two atom indexes
A deg angle between three atoms specified by three atom indexes
D deg dihedral angle between four points specified by four atom indexes

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
CVS
2
1 D   169.9998  5  8 11 13
2 B     1.3456  5 11
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