[gmx-users] trjconv:solute at the center
ndhumal at andrew.cmu.edu
Mon Oct 17 21:18:27 CEST 2011
Ya, I want to center solute w.r.t to the solvent.
I have more question, if I want to save the coordinates of a snapshot with
no pbc effect, can I use -pbc nojump in trjconv.
On Mon, October 17, 2011 1:34 pm, Tsjerk Wassenaar wrote:
> Hey :)
> The reference plays no role in centering. But I guess that Nilesh expects
> centering of the solute w.r.t. to the solvent, or is looking at the
> wrong center (tric/rect).
> On Oct 17, 2011 7:06 PM, "Justin A. Lemkul" <jalemkul at vt.edu> wrote:
> Nilesh Dhumal wrote: > > Thanks Justin, > > Still solute is not at
> center. >
> Is your reference frame (i.e. the .tpr file) centered? If not, centering
> likely won't work as desired. I assumed that it was centered, per
> normal system building procedures.
>> Nilesh > > > On Mon, October 17, 2011 11:27 am, Justin A. Lemkul wrote:
>>> Nilesh Dhumal wrote...
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