Problem with .conf file of NAMD

From: sudipta sinha (sudipta.mml_at_gmail.com)
Date: Mon Jun 16 2008 - 06:30:57 CDT

Hi All,

        I have question regarding the input file of NAMD simulation. Suppose
I want to continue a simulation by restart files. If in my .conf file,
binaryoutput is no then I am getting a PDB formatted restart file but when
it is yes then I am getting a binary coordinate file. Now when I want to
continue my simulation by PDB formatted the restart file then it is
running ok. But when I want to run by the binary coordinate file then an
additional PDB formatted coordinate file is require. So by inserting
the binary coordinate restart along with a PDB formatted coordinate the
simulation is running. So my question what is the basic difference between
them? or are both of these simulation same? Although in NAMD user guide
second method is recommended due to the accuracy of binary files rather
ASCII PDB file. and also what is the function of PDB file in second
method. If I want to use second method then which PDB file can I use? Is it
the initial PDB file? I want to get some needful suggestions. Awaiting for
your early reply.

Thanks and regards
Sudipta

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