[gmx-users] PBC

[Sai Kumar Ramadugu]

Hi Morteza,
  I had this problem when I was running a trimeric protein attached to an
oligosaccharide.

*I have used the following command:*

* *

*trjconv  -s .tpr -f .xtc -o   -boxcenter tric -pbc mol*

* *

*but it is not working.*


Do the following. It worked for me.


In the first round, run

trjconv -f *.xtc -s *.tpr -center -boxcenter tric -pbc mol -o 1.xtc

and choose backbone (which is usually 4 from the index) for centring.


In the second round,

use 1.xtc obtained from the first step and run the command as follows


trjconv -f 1.xtc -s *.tpr -center -boxcenter tric -pbc a -o 2.xtc

and this time also choose the backbone for centring.


This should bring back the dimeric protein system in the box. Sometimes the
water molecules around the edge are broken. Hope this is not a big worry.


By the way is your box cubic or truncated octahedron?

My case was a cubic box.


Hope this helps.


Regards

Sai


On Tue, Jun 8, 2010 at 2:23 AM, shahab shariati
<shahab.shariati at gmail.com>wrote:

> Morteza Khabiri wrote:
>
>
>
> Dear users
>
>
>
> I have a dimer protein in the water box. It was run for 30ns.
>
> during the simulation dimer split to two monomer. This things happen bc of
>
> PBC. ( I checked it by vmd pbc option )
>
> to have a two monomer together during trajectories (for visualization)
>
> I have used the following command:
>
>
>
> trjconv  -s .tpr -f .xtc -o   -boxcenter tric -pbc mol
>
>
>
> but it is not working.
>
> Is there any other method or command which I could implement pbc in
>
> trajectory.
>
>
>
> Thanks in advance
>
>
>
> Morteza
>
>
>
>
>
>
>
> Shahab Shariati wrote:
>
>
>
> You can use other flags of trjconv command as follows:
>
>
>
> Trjconv –f *.xtc –s **.tpr –o ***.xtc –pbc nojump –ur compact -center
>
>
>
>
>
>
>
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