Dear Irem,
You may want to run the trajectory through trjconv and translate it, or use
e.g. -pbc whole, so that the protein is intact at frame 1. Then you can run
trjconv -pbc nojump on the resulting trajectory. This usually requires a bit of
trial and error.
Kind regards,
Erik
> On 31 Mar 20
I think the problem is that I can’t seem to start from an unfragmented
structure. I start from the .pdb file, where the protein is a whole, and end up
with a .tpr file that is fragmented. The interesting thing is, this did not
happen with version 4.6.5 (I now use 5.1.2). Do I have to do somethin
No! You can't do that, because fitting will cause the PBC and the
coordinates to mismatch. So 'nojump' after that will for sure screw up the
coordinates. Check the trjconv workflow on the Gromacs site.
Cheers,
Tsjerk
On Mar 31, 2016 14:23, "Francesco Carbone" wrote:
> You could try to fit first
Hi,
Thanks. If I do that, the reference structure would be what’s in the .tpr file,
right?
Best,
Irem
> On Mar 31, 2016, at 8:22 AM, Francesco Carbone wrote:
>
> You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump) later.
>
> Cheers,
>
> Fra
>
> On 31 March 2016 at 05:45,
Hi,
Thanks for your suggestion. Unsurprisingly, the structure in
nvt_water_frozen.tpr is also fragmented. Is there a way to use the input .pdb
file as reference, somehow?
Best,
Irem
> On Mar 31, 2016, at 12:45 AM, Tsjerk Wassenaar wrote:
>
> Hi Irem,
>
> Check the structure in nvt_water_fro
You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump) later.
Cheers,
Fra
On 31 March 2016 at 05:45, Tsjerk Wassenaar wrote:
> Hi Irem,
>
> Check the structure in nvt_water_frozen.tpr:
>
> gmx editconf -f nvt_water_frozen.tpr -o ref.pdb
>
> Cheers,
>
> Tsjerk
> On Mar 31, 2016 0
Hi Irem,
Check the structure in nvt_water_frozen.tpr:
gmx editconf -f nvt_water_frozen.tpr -o ref.pdb
Cheers,
Tsjerk
On Mar 31, 2016 00:04, "Irem Altan" wrote:
> Hi,
>
> I am simulating a protein in its unit cell. I use the original .pdb file
> as an input, so the initial molecule is not frag
Hi,
I am simulating a protein in its unit cell. I use the original .pdb file as an
input, so the initial molecule is not fragmented. At the end of the simulation,
I generate a .pdb file containing the trajectory of the protein as follows:
gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.
