PROFASI  Version 1.5
Initial structures in PROFASI simulations

Almost all our simulations start with random initial values assigned to all degrees of freedom. In a few instances we have used a "stretched" chain as the starting point. It is however a frequent request that it should be possible to start simulations from a given initial structure. Here we describe how that can be done.

Random and stretched initial conformations

To start simulations from random configuration of the protein chains, you don't have to do anything about the start configuration. That is the default behaviour.

To start from stretched chains, use the command init_config in the settings file.

add_chain 1 <*GEWTY DDATKT FTVTE*>
init_config stretched

Simulation programs based on BasicMCRun, such as SimTempRun, SimAnnealRun, ParTempRun and WLRun store the starting structure for the simulations in a file called start.xml. Each rank in a parallel run stores its own start conformation. Normally, the start conformations are stored after the so called "preliminary relaxation" cycles. These are normal MC cycles at a high temperature to remove atom clashes, so that in the main loop of the simulation, the energies start at reasonable values. The number of relaxation cycles is 10 times the number of chains in the system. This is the reason why even when you specify "stretched" as init_config, you don't see a flat elongated chain as the start structure.

Remember that "stretched" does not really mean using a physical stretching force and determining the stretched protein conformation. It simply assigns values to the degrees of freedom such that the chain appears extended. It is not guaranteed that a stretched conformation in this sense wont lead to clashes between atoms. Therefore the relaxation cycles are run even for stretched starts. It is possible to use a settings file command to skip the relaxation cycles, so that init_config stretched will produce a stretched start.xml file.

add_chain 1 <*GEWTY DDATKT FTVTE*>
init_config stretched
preliminary_relaxation off

Starting from a given structure

Here we are talking about starting the simulations from, for instance, a PDB file. Suppose you have a PDB file abc.pdb and you want a simulation to start from that structure. Follow these steps:

The above illustrates the principle. The recommended way to provide a starting structure is to use a structure in PROFASI's XML structure file format. The programs regularize and prf_convert can be used to generate such a structure from a given PDB file. Regularize does more than just the format conversion, and is recommended unless the PDB file was generated in a PROFASI simulation. The XML structure file can also be extracted from a previous simulation with PROFASI using the program extract_snapshot .

See Also
Regularization: approximating a protein structure , extract_snapshot , Converting between structure file formats, PROFASI's XML structure file format

PROFASI: Protein Folding and Aggregation Simulator, Version 1.5
© (2005-2016) Anders Irbäck and Sandipan Mohanty
Documentation generated on Mon Jul 18 2016 using Doxygen version 1.8.2