> I have done a MD simulation and would like to examine the normal vector as
> a function of time for three different atoms in the same residue. I
> am trying to do this using CARNAL. From the manual, and my own attempts,
> I gather that the vector formed by the PLANE command is not a MEAS that
> can be output.
It would be interesting to see what you tried. I think that if you
list the plane in an OUTPUT TABLE statement the vector should appear
in the table.
> Alternatively, I could just output the coordinates of the
> three atoms as a function of time and calculate the vector myself. I
> assume this is done by a GROUP command following the DECLARE statement and
> an additional statement following the OUTPUT command. I cannot get this
> to work. Could someone point me in the right direction to outputting the
> coordinates as a function of time?
The group id would have to be in an OUTPUT COORD statement or some
such.
If ptraj can do this, it might be better to use it since the plan
is to drop carnal from future distributions, and since no one outside
the amber group has expressed an interest in maintaining it, I expect
it might sink out of sight fairly soon.
Bill
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Received on Fri Apr 15 2005 - 18:53:00 PDT
