[gmx-users] peptide out of water box after em

Chris Gaughan clgaughan68 at yahoo.com
Mon Sep 26 00:41:43 CEST 2005


I am trying simulate dimer formation with two
peptides. Both peptides were separately energy
minimized in water and then concatenated. I took out
the waters and translated one of the peptides so they
were about 0.5 nm apart. I put them in a 4 nm box and
with spc water- both peptides are in this box.
However, when I do the energy minimization, one of the
peptides is situated outside the water box. This
happens in the in vacuo em as well. Can someone help
me understand this?


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