I have been working through some sample problems and now I am at the stage
where I need to settle on a consistent setup for simulation of short peptides
in aqueous solution. I've been through the documentation repeatedly, but there
are a couple things on which I am unclear.
1) I am going to use the OPLS/AA force field, and as per the manual I will
use the TIP4P water model, and the PME method. However, when it comes to
choices for rcoulomb, rlist and rvdw I am not clear. The first OPLS/AA force
field paper (Jorgensen et al 1996) that I can find doesn't have an explicit set
of cutoffs, different cutoffs are specified for different organic liquids, and
the PME section of the manual doesn't suggest values. So what are the
recommended values for rcoulomb, rlist and rvdw when using the OPLS/AA force
field and PME calculation? I've been using 1.0 for all three up to now.
2) Since I am looking at short peptides, I am not sure what the best way
is to define box size. The extreme version is to assume a fully extended
peptide backbone at 0.35 nm/residue and make the box diameter that length plus
2X the cutoff values. However, that makes a generally excessively large box,
since the fuly extended conformation is very unlikely to ever occur. Is there
some rule of thumb for specifying the smallest box that will avoid interactions
between the instances of the peptide in different cells?
Thanks for any and all advice.
Warren Gallin--
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