Simulations: Difference between revisions
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basic outline of how to run simulations |
-> bash script |
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The standard protocol is: | The standard protocol is: | ||
# make a working directory | # make a working directory | ||
# copy your input files (pdb and hippo_input.txt) into the working dir | # copy your input files (pdb and <tt>hippo_input.txt</tt>) into the working dir | ||
# (optional) copy your executable | # copy the hippo data files (<tt>oplsaa_forcefield.dat</tt> and <tt>hippo_protein_database.dat</tt>) into the working dir | ||
# (optional) copy your executable into the working dir | |||
# start hippo <pre>hippo</pre> | # start hippo <pre>hippo</pre> | ||
Hippo will load the pdb, build an internal topology, and then run the simulation. It will inform of its progress and its estimated finishing time. | Hippo will load the pdb, build an internal topology, and then run the simulation. It will inform of its progress and its estimated finishing time. | ||
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If there are problems, look at the <tt>log.txt</tt> output file. | If there are problems, look at the <tt>log.txt</tt> output file. | ||
Steps 1-4 can be automated with the bash script [[hippo_setup.sh]]. | |||
[[Category:Hippo]] | [[Category:Hippo]] | ||
[[Category:Howto]] | [[Category:Howto]] | ||
Latest revision as of 20:15, 18 October 2008
This page should help you running simulations with Hippo.
To run a simulation you will need
- hippo executable and data files in a directory which we will denote by HIPPO_HOME
- a pdb file for your system
- a hippo_input.txt
The standard protocol is:
- make a working directory
- copy your input files (pdb and hippo_input.txt) into the working dir
- copy the hippo data files (oplsaa_forcefield.dat and hippo_protein_database.dat) into the working dir
- (optional) copy your executable into the working dir
- start hippo
hippo
Hippo will load the pdb, build an internal topology, and then run the simulation. It will inform of its progress and its estimated finishing time.
If there are problems, look at the log.txt output file.
Steps 1-4 can be automated with the bash script hippo_setup.sh.
