Applications/Packmol - Revision history

Pysdlb: /* Further Information */

2022-11-17T13:50:04Z

‎Further Information

Pysdlb: /* Usage Examples */

2022-11-17T13:49:41Z

‎Usage Examples

Pysdlb: /* Navigation */

2022-11-16T10:54:46Z

‎Navigation

Pysdlb at 13:30, 24 May 2019

2019-05-24T13:30:24Z

Pysdlb: Pysdlb moved page Application/Packmol to Applications/Packmol without leaving a redirect

2018-12-05T10:15:06Z

Pysdlb moved page Application/Packmol to Applications/Packmol without leaving a redirect

Pysdlb: Created page with "TOC ==Application Details== * Description: PACKMOL creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The pack..."

2018-12-05T10:11:45Z

Created page with "__TOC__ ==Application Details== * Description: PACKMOL creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The pack..."

New page

__TOC__

==Application Details==

* Description: PACKMOL creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short range repulsive interactions do not disrupt the simulations.
* Version: 18.169 (compiled with intel/2018)
* Modules: packmol/intel/18.169
* Licence: Open source (Github)

==Introduction==

PACKMOL creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short range repulsive interactions do not disrupt the simulations.

The great variety of types of spatial constraints that can be attributed to the molecules, or atoms within the molecules, makes it easy to create ordered systems, such as lamellar, spherical or tubular lipid layers.

The user must provide only the coordinates of one molecule of each type, the number of molecules of each type and the spatial constraints that each type of molecule must satisfy.

The package is compatible with input files of PDB, TINKER, XYZ and MOLDY formats.

==Usage Examples==

===Interactive session===

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

[pysdlb@login01 ~]$ interactive
salloc: Granted job allocation 1211823
Job ID 1211823 connecting to c095, please wait...
[pysdlb@c095 ~]$ module load packmol/intel/18.169
[pysdlb@c095 ~]$ packmol < mixture.inp

################################################################################

PACKMOL - Packing optimization for the automated generation of
starting configurations for molecular dynamics simulations.

Version 18.169

################################################################################

Packmol must be run with: packmol < inputfile.inp

Userguide at: www.ime.unicamp.br/~martinez/packmol

Reading input file... (Control-C aborts)
Seed for random number generator: 1234567
Output file: mixture.pdb
Reading coordinate file: water.pdb
Reading coordinate file: urea.pdb
Number of independent structures: 2
The structures are:
Structure 1 :water.pdb( 3 atoms)
Structure 2 :urea.pdb( 8 atoms)
Maximum number of GENCAN loops for all molecule packing: 400
Total number of restrictions: 2
Distance tolerance: 2.00000000000000

</pre>

==Further Information==

* [http://m3g.iqm.unicamp.br/packmol/home.shtml http://m3g.iqm.unicamp.br/packmol/home.shtml]

{|
|style="width:5%; border-width: 0" | [[File:icon_home.png]]
|style="width:95%; border-width: 0" |
* [[Main_Page|Home]]
* [[Applications|Application support]]
* [[General|General]]
* [[Training|Training]]
* [[Programming|Programming support]]
|-
|}

@@ Line 81: / Line 81: @@
 </pre>
-==Further Information==
+==Next Steps==
 * [http://m3g.iqm.unicamp.br/packmol/home.shtml http://m3g.iqm.unicamp.br/packmol/home.shtml]
 {{Modulepagenav}}

← Older revision		Revision as of 10:54, 16 November 2022
Line 63:		Line 63:
	* [http://m3g.iqm.unicamp.br/packmol/home.shtml http://m3g.iqm.unicamp.br/packmol/home.shtml]		* [http://m3g.iqm.unicamp.br/packmol/home.shtml http://m3g.iqm.unicamp.br/packmol/home.shtml]

−	~~==Navigation==~~	+	{{Modulepagenav}}
−
−	* [[Main_Page\|Home]]
−	~~* [[Applications\|Application support]] *~~
−	* [[General\|General]]
−	* [[Programming\|Programming support]]

@@ Line 25: / Line 25: @@
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
-[pysdlb@login01 ~]$ interactive
+[username@login01 ~]$ interactive
 salloc: Granted job allocation 1211823
 Job ID 1211823 connecting to c095, please wait...
-[pysdlb@c095 ~]$ module load packmol/intel/18.169
+[username@c095 ~]$ module load packmol/intel/18.169
-[pysdlb@c095 ~]$ packmol < mixture.inp
+[username@c095 ~]$ packmol < mixture.inp
 ################################################################################
@@ Line 48: / Line 48: @@
    Output file: mixture.pdb
    Reading coordinate file: water.pdb
-   Reading coordinate file: urea.pdb
+   Reading coordinate file: urea.pdbmodule load packmol/intel/18.169
    Number of independent structures:            2
    The structures are:
@@ Line 56: / Line 58: @@
    Total number of restrictions:            2
    Distance tolerance:    2.00000000000000
 </pre>

@@ Line 63: / Line 63: @@
 * [http://m3g.iqm.unicamp.br/packmol/home.shtml http://m3g.iqm.unicamp.br/packmol/home.shtml]
 * [[Main_Page|Home]]
-* [[Applications|Application support]]
+* [[Applications|Application support]] *
 * [[General|General]]
 * [[Programming|Programming support]]

← Older revision	Revision as of 10:15, 5 December 2018
(No difference)