[gmx-users] trjconv:solute at the center

[Nilesh Dhumal]

Thanks Justin,

Still solute is not at center.

Nilesh


On Mon, October 17, 2011 11:27 am, Justin A. Lemkul wrote:
>

>
> Nilesh Dhumal wrote:
>
>> In 2nd step I choose system instaed of solvent.
>>
>>
>> I could not make the solute at the center.
>>
>>
>
> Don't use -b and -e when running trjconv.  I have found that PBC routines
> are not always correctly applied when parsing out sections of the
> trajectory.  This can affect your ability to center the molecule.
>
> -Justin
>
>
>> Thanks
>> NIlesh
>>
>>
>> On Mon, October 17, 2011 11:05 am, Justin A. Lemkul wrote:
>>
>>
>>> Nilesh Dhumal wrote:
>>>
>>>
>>>> Justin,
>>>>
>>>>
>>>>
>>>> I have 26 solute atoms and 3302 solvent atoms in my sytems (total
>>>> 3328
>>>> atoms).
>>>>
>>>>
>>>> 1. trjconv -f 3.trr -s 3.tpr -pbc mol -b 400 -e 600 -dt 1 -n
>>>> 500-1.ndx
>>>> -o
>>>> 4-600.xtc
>>>> here I choose group 0:system (3328 atoms)
>>>>
>>>> 2. trjconv -f 4-600.xtc -s 3.tpr  -n 500-1.ndx -center  -o
>>>> 4-600-1.xtc
>>>>
>>>>
>>>>
>>>> For Centering I choose group: solute (26 atoms)
>>>> For output I choose group : Solvent (3302 atoms)
>>>>
>>>>
>>>>
>>>>
>>>> 3. trjconv -f 4-600-1.xtc -s 3.tpr  -dump 500  -o 500-11.pdb
>>>>
>>>>
>>>>
>>>> Here I choose the group: 0 (system).
>>>>
>>>>
>>>>
>>>> I am geting for error for last command.
>>>>
>>>>
>>>>
>>>> Fatal error:
>>>> Index[3302] 3303 is larger than the number of atoms in the
>>>> trajectory file (3302).
>>>>
>>>>
>>>> It look that there are no solute atoms in trajectory file.
>>>>
>>>>
>>>>
>>> In step 2, you chose to save only the solvent.
>>>
>>>
>>>
>>> -Justin
>>>
>>>
>>>
>>> --
>>> ========================================
>>>
>>>
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>>
>>>
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>>>
>>
>>
>>
>
> --
> ========================================
>
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
> ========================================
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