User Information

How To Run ProtoMol

Running ProtoMol:

./protomol 3mg7ca.conf

In order to get help:

./protoml -h

To figure out the supported forces:

./protoml -f

To figure out all possible input / output keywords:

./protoml -k

Man alike:

./protomol -m keyword

or to print all possible keywords

./protomol -m --keywords

GUI Front-End: TkProtoMol.pl

ProtoMol's TkProtoMol.pl offers a simple GUI (perl/Tk) to edit configuration files, run simulations, and visualize output data.

Installing perl/Tk

Windows:
- Download and install perl from ActiveState
Linux/Unix:
- Download perl/Tk 804.027
- Create a directory where you place your perl packages ($HOME/perl/packages)
- Install your packages with prefix $HOME/perl
- Add your modules/packages with export PERL5LIB=$HOME/perl/lib/perl5:$HOME/perl/lib/perl5/site_perl to your environment
Perl documentation
CPAN modules
Installing Your Own Perl Modules
ActiveState PPM's
PPM Repository (Windows)

Visualization

ProtoMol's xyzviz is a simple visualization application tool based on OpenGL/GLUT, which reads all kind of coordinate format files. It supports trajectories and writing frames to be assemble to movies and EPS.

Furthermore, ProtoMol writes DCD files, which can be read by VMD.