[gmx-users] trjconv:solute at the center

[Nilesh Dhumal]

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.

Nilesh


On Mon, October 17, 2011 7:25 am, Justin A. Lemkul wrote:
>

>
> Nilesh Dhumal wrote:
>
>> Hello,
>>
>>
>> I have system with solute is surrounded by 256 solvent molecules. I run
>>  the simulation for 20 ns. I save the snap shot at 500 ps using
>> following command.
>>
>> trjconv -f 3.trr -s 3.tpr -n 500-1.ndx -b 500.0 -e 501.0 -dt 1.0 -pbc
>> nojump -center   -o 500-11.pdb
>>
>> I tried to keep the solute at the center box. In visualization, the
>> solute is not at center , its close to box edges.
>>
>> How can I keep the solute at the center.
>>
>>
>>
>
> You're doing too many things at once.  Split the trjconv operation:
>
>
> 1. Run trjconv -pbc mol on the whole trajectory
> 2. Run trjconv -center on the output of (1)
> 3. Run trjconv -dump 500 on the output of (2)
>
>
> -Justin
>
>
>> I am using Gromacs 4.0.7 version.
>>
>>
>> Thanks
>>
>>
>> Nilesh
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
> --
> ========================================
>
>
> 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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