Some basics 1st - The extended system file in NAMD, is the file that stores the box size information. Once a simulation has reached it's number of simulations steps, it will write a set of files to restart from, containing:
*.coor
i replaced the cell dimension by box size dimension using findbox.tcl file yet it unable to read .xsc file.
i am attaching the config file, could you please pin point what are the shortcomings in the same. i hv been stumbling over one step or other to minimize the system. it would be great help.
thanks..
Some notes:
For the first stage of a simulation, usually a minimization, you don't need any restart files. You use your initial PDB as "coordinates". Velocities are not used during minimization and the initial box is given by CellBasisVector1-3 and will not change during minimization. The minimization is meant to remove any odd atomic clashes due to system building.
Afterwards, one can perform equilibration MD. Here you 1st create new random velocities by "reinitvels". The run command afterwards performs the MD simulation. You usually use the NVT ensemble here, so temperature control by e.g. the langevin thermostat.
Then, you can also continue a simulation by using its restart files as input in a new namd config file. Here you would define "ccordinates" "velocities" and "extendedsystem" to the respective "coor" "vel and "xsc" of the former simulation. Since you already have velocities and the box, you dont have "temperature" or "reinitvels" "CellBasisVector1-3" in such a namd config. The next stage is usually a NPT equilibration run (e.g. langevinpiston barostat), to adapt the box density.
Finally you run from the restarts of the NPT stage, the actual production MD.
Btw. you need to learn understanding the NAMD error messages ;)
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