[gmx-users] trjconv:solute at the center

[Justin A. Lemkul]

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

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