[gmx-users] trjconv:solute at the center

[Tsjerk Wassenaar]

Hi Nilesh,

To center the solute with respect to the solvent, first center the
solute in the box, and then put the solvent in the box. Mind that that
involves two passes of trjconv.

If 'no pbc effect' means no wrapping over the boundaries, yes you can
use -dump with -pbc nojump to save a snapshot. trjconv will go over
the frames and 'unwrap' the frames before the snapshot you want.

Hope it helps,

Tsjerk

On Mon, Oct 17, 2011 at 9:18 PM, Nilesh Dhumal <ndhumal at andrew.cmu.edu> wrote:
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands