[gmx-users] trjconv:solute at the center

[Justin A. Lemkul]

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
> 
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-- 
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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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