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

[Dallas B. Warren]

Chris,

> 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?

Is it a long way out of the box, or totally out of contact with the
water?  Or is some of it submerged into the water?  If the latter, then
it is just a PBC issue, former no idea.

Catch ya,

Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9073
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