General question about NAMD

From: michael jerry (mike.sean_at_gmail.com)
Date: Tue Nov 08 2005 - 10:52:04 CST

I am now shifting from CHARMM to NAMD. I have a few questions about how to
use NAMD.

1. PBC
I use the coordinate and structure files generated from CHARMM as the input
of NAMD. For the PDB coordinates, the origin in the CHARMM was set in the
center of box. In the NAMD, I don't know where is origin? it is in the
center of the cell or in the left-corner of the cell. For example,
CellBasisVector1 60.0 0.0 0.0
CellBasisVector2 0.0 60.0 0.0
CellBasisVector3 0.0 0.0 60.0
CellOrigin 0.0 0.0 0.0 or CellOrign 30.0 30.0 30.0??

which one I should use when I turn on "wrapall" option?

2. heating or equlibrium
For the heating,
temperature 0.0
reassignFreq 100
reassignTemp 20.0
reassignIncr 20.0
reassignHold 300.0

For the equlibrium
temperature 300

am I right?

3. xstfile
For the NVT system, do I need to write xstfile regularly in terms of
xstfreq? Do the cell box information include in the restart file? I knew if
I turn on "DCDunitcell" option, the cell dimension will be writtten in the
DCD file. But for the restart, I am not so sure.

I will appreciate for any help from you.

By the way, it should be great if NAMD put some sample scripts, including
minimization, heating, and equilbrium for the NVT, NPT systems with
different temperature and pressure control methods. Just like the CHARMM
does. I can lower the learn curve and trigger more people to use NAMD. just
my two cents.

thanks.

Sean

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