[Top][All Lists]

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[ESPResSo-users] "emoltemplate" molecule builder for ESPResSo (TCL)

From: Andrew Jewett
Subject: [ESPResSo-users] "emoltemplate" molecule builder for ESPResSo (TCL)
Date: Thu, 8 Dec 2016 21:22:53 -0800

   A molecule builder for ESPResSo has been released at:

   This program generates a list of TCL commands containing atom coordinates, bonded interactions and force-field parameters for any molecule that you can simulate in ESPResSo.  Emoltemplate is not a tool for building molecules that use a particular type of force-field (eg AMBER, OPLS, GROMOS), Martini).  Emoltemplate was designed for building complex heterogeneous (hierarchical) biological coarse-grained models.  No assumptions are made about the form of the potential used.  This should work with new force-field styles added to ESPResSo in the future.

   Emoltemplate is also a file format for storing and sharing force-fields.  Force-field files saved in "emoltemplate" (".et") format can contain user-definable rules can be used to generate angle, dihedral, and improper interactions and lookup their corresponding force-field parameters.  The user has complete control over how this is done.

   "Emoltemplate" is similar to ("moltemplate"), a molecule builder for LAMMPS.  The two programs use similar syntax and share a lot of the same code.  Due to the extensive testing (of the LAMMPS version) over the last couple years, both programs are quite stable.  Both programs also come with examples, however there are not yet very many examples that make use of ESPResSo.  (This is an area that needs improvement.  If you find this program program useful, feel free to send me examples of molecules or force-fields, and I will post them.)



   Python limitations:
Emoltemplate does not currently take advantage of ESPResSo's python interface.  (Emoltemplate could be modified to generate python instead of tcl commands by rewriting the "" and "" files, containing approximately 1000 lines of code.  I can help with the conversion if there is demand for this.)

reply via email to

[Prev in Thread] Current Thread [Next in Thread]