Dear Users,
It works with the following command.
> trjconv -f confout.gro -o output.gro -pbc whole
Thank you.
Best regards,
Changwoon Jang
On Fri, Aug 26, 2016 at 9:21 AM, Marlon Sidore
wrote:
> Hello,
>
> If you want your molecule whole, the -pbc mol option of trjconv is probably
> wha
Hello,
If you want your molecule whole, the -pbc mol option of trjconv is probably
what you're searching for.
Marlon Sidore
PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
France
2016-08-26 15:05 GMT+0
Dear Justin Lemkul,
Thank you. I am going to try it. I tried to understand trjconv via the
manual.
Best regards,
Changwoon Jang
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On 8/25/16 11:36 PM, Chang Woon Jang wrote:
Dear Gromacs Users,
I would like to describe the situation. An initial molecule in the
periodic boundary condition is located near the right side of box. The box
is big, thus needs to be adjusted and equilibrated under NPT. The box
should be shrin
Dear Gromacs Users,
I would like to describe the situation. An initial molecule in the
periodic boundary condition is located near the right side of box. The box
is big, thus needs to be adjusted and equilibrated under NPT. The box
should be shrinked after few ns seconds. The molecule near the
You can use VMD to visually wrap the molecules by typing:
pbc wrap -compound res -all
In the command interface on VMD.
-Evan L.
On Aug 25, 2016 8:06 PM, "Chang Woon Jang" wrote:
> Dear Sir,
>
>Attached are figures here.
>
> Thank you.
>
> Best regards,
> Changwoon Jang
>
> --
> Gromacs Us
On 8/25/16 10:06 PM, Chang Woon Jang wrote:
Dear Sir,
Attached are figures here.
The mailing list does not accept attachments. Follow the previous link about
PBC and consult Google. Using trjconv comes up daily on this mailing list.
-Justin
--
==
Dear Sir,
Attached are figures here.
Thank you.
Best regards,
Changwoon Jang
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Hi,
I can't find your figures and I guess this link may be helpful to you:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
On 26 August 2016 at 09:49, Chang Woon Jang wrote:
> Dear Gromacs Users,
>
> Sorry for the misspelling of "Grimaces Users" due to automatic
Dear Gromacs Users,
Sorry for the misspelling of "Grimaces Users" due to automatic
predictive text function. I am waiting for the answer.
Thank you.
Best regards,
Changwoon Jang
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Dear Grimaces Users,
When I run a simulation with NPT under periodic boundary condition, the
output file (confout.gro) is obtained with shrinked box due to the external
pressure. Because of the periodic boundary condition, some molecules might
be cross the boundary appearing the other side of b
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