> I try to resend my email that probably was not read/received.
> Any hint to fix my RMSD values would be really appreciated.
There is probably not an easy way to fix. Look through the archive as
suggested about imaging issues and try things like center only the first
residue of each chain, etc. and imaging. Imaging based on the first atom
rather than center of mas, etc.
This was what prompted the question on the reflector back to you about box
size / amount of solvent. Likely there is too little, so there is not an
easy way to, by generic procedure, image the molecules back since the
periodic image may be closer than the unit cell, i.e. once it is wrapped,
it becomes closer to its image.
I have been meaning to write a smarter imaging routine that would attempt
to minimize distances, however I have not done this.
There are ways to make it so all the molecules are together in the prmtop
which will prevent this.
--tec3
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Received on Tue Sep 27 2011 - 14:00:02 PDT
