On Mon, Oct 01, 2012, Kepa K. Burusco wrote:
>
> So, just to be sure that I understood you correctly: if I run a TI
> simulation asking for jfastw=0 (by default), ntc=1 and ntf=1, do you
> mean that "sander" automatically recognises TIP3P water molecules as
> RIGID ones by default and does the calculation SHAKEing the solvent but
> not the solute? Because this is the case I am interested in.
No, this is not correct. If you want to avoid shake in part or all of the
solute, turn SHAKE on (with ntc=2), but use the noshakemask string to turn off
shake for any parts of the solute where the atom types are changing between V0
and V1.
....dac
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Received on Sun Sep 30 2012 - 19:00:03 PDT
