Keep discussions on the list. I am not your personal help. I will not
respond to future e-mails to my personal address.
Type `gmx trjconv -h` and read.
Also read
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
On 29-05-17 13:43, Dilip H N wrote:
> Thank you...
>
Keep discussions on the list.
As i wrote in my previous mail, you need `gmx trjconv -pbc mol -center
...`. In your example this would be:
> gmx tjrconv -f md.xtc -s md.tpr -pbc mol -o mdx.xtc *-center*
> vmd mdx.xtc
If you can't figure it out from here, try `gmx trjconv -h` and read.
Peter
Hi,
I would not do this. I would run my simulation as normal (no position
restraints), and center my amino acid in post processing (gmx trjconv
-pbc mol -center ...). You may need to make an appropriate index file.
Alternatively you may want to use -fit instead of -center, but that's a
matter of
Hi Dilip,
To fix the amino acid at the centre of the box first you have to use -c
flag with editconf. Later, during simulation you have to use
define=-dposres in the mdp file. This will include the position restrain
defined in the posre.itp file generated during the use of pdb2gmx.
Best,
Saumyak
Hello,
I have ran a md simulation of a amino-acid with solvent mixture. Now i view
the trajectory in vmd and see tht the amino-acid moves sometimes toward the
edge of the box,sometimes towards the corners and so on...
Now how can i centre only the amino-acid to the centre of the box and rest
