[gmx-users] trjconv:solute at the center

[Justin A. Lemkul]

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:
>>
>>> 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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>>
> 
> 
> 

-- 
========================================

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

========================================