PME and fixed atoms questions

From: Christopher Hartshorn (
Date: Mon Mar 09 2009 - 13:31:52 CDT

Hello all. I have two questions:

1) In one of my sims, after about 2ns I noticed that many of the Na
and Cl ions were way off in space relative to the rest (e.g. their are
about 30 ions way beyond the borders of the water box, as in 50
angstroms away in each direction). Now, I assume this happened
because I "wrapped" only the water, but I am not sure whether this is
a problem to my PME calculations. I have checked and seen that
the .xsc file still is only registering the correct xyz-lengths for
the water box only. Thus, my question is will these ions, since they
are not in the cube that the PME is calculated from, have a
detrimental effect upon the PME calculations/time step because the
system is no longer electrostatically neutral (since there are 30 less
ions in the actual PBC box then after the system was ionized) or are
these still "seen" by the PME calculations?

2) I have a subset of my atoms that I have kept as fixedatoms.
Originally, I kept fixedatom forces=on because I was under the
impression that doing so would allow everything surrounding the
fixedatom set to feel the forces of the fixedatoms (e.g. nonbonded
forces). But after reading the NAMD manual again, I am not sure what
the fixedatom forces actually does. Does having this feature on make
sure that all forces (bonded/nonbonded) remain on without allowing
movement of the atoms or does having this on only turn on the bonded
forces because the nonbonded are always active and accounted for? In
simpler terms, do I need to have this feature on if all I want is for
the rest of system to feel the nonbonded forces of this subset of

As always Thank you for any and all help.



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