Here, I have attached a conf file for the minimization of my structure in NAMD. From my previous experience of working with Gromacs, it uses the output of the minimization for equilibration and hence production run. But, after running minimization in NAMD, it does not give me minimized system which I can use for production run in NAMD. So, does it mean that my previous pdb file (ionized.pdb) has been minimized or I should have got other file (.pdb) after minimization.
To get a pdb, you can load the dcd file into vmd and then save the last frame as pdb.
the minimized structure coordinates will be stored in the "coor" file. In your subsequent NAMD files, you need to load these coordinates by adding
bincoordinates filename.coor
to your scrip just after loading the psf file.
Sir, is there any way to get the minimized structure coordinates in pdb format rather than in .coor format ? I used binaryoutput no in my configuration file to obtain the .coor in plain text format rather than in binary format which I renamed into .pdb file to get pdb format. But, are there are changes that we can make in our configuration to obtain the minimized structure coordinates directly.
To get a pdb, you can load the dcd file into vmd and then save the last frame as pdb.
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