[gmx-users] trjconv:solute at the center

[Nilesh Dhumal]

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.

nilesh

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).
>
> Cheers,
>
>
> Tsjerk
>
>
> 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.
>
> -Justin
>
>
>> Nilesh > > > On Mon, October 17, 2011 11:27 am, Justin A. Lemkul wrote:
>> >
>>
>>> Nilesh Dhumal wrote...
>>>
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