Hi,
On Thu, Jun 22, 2017 at 3:57 PM Diez Fernandez, Amanda <
amanda.die...@imperial.ac.uk> wrote:
> Hi Mark,
>
> Thanks.
>
> >mdrun will generally "make molecules whole" for -c, but otherwise doesn't
> >care. Implementing general triclininc 3D periodicity with domain
> >decomposition is a messy
Hi Mark,
Thanks.
>mdrun will generally "make molecules whole" for -c, but otherwise doesn't
>care. Implementing general triclininc 3D periodicity with domain
>decomposition is a messy business.
I am not using a triclinic unit cell (all angles are 90 in the input .pdb
file). Wouldn¹t the
Hi,
On Thu, Jun 22, 2017 at 11:05 AM Diez Fernandez, Amanda <
amanda.die...@imperial.ac.uk> wrote:
> Hi Mark,
> Thank you for your reply.
>
> It is exactly the opposite though:
OK, I understood the images the other way around, without titles.
> for output_coordinates.gro which is the
>
-
>
>Message: 1
>Date: Wed, 21 Jun 2017 17:29:53 +
>From: Mark Abraham <mark.j.abra...@gmail.com>
>To: gmx-us...@gromacs.org
>Subject: Re: [gmx-users] Difference between output_coordinates.gro and
> trajectory.xtc coordinates
>Message-ID:
>
Hi,
On Wed, Jun 21, 2017 at 6:49 PM Diez Fernandez, Amanda <
amanda.die...@imperial.ac.uk> wrote:
> Hi Justin,
> Thank you for your reply.
>
> Here are the links to the images of:
> -the output coordinates
> -and last frame of trajectory.
>
> Output coordinates which look wrong:
>
am looking something like [ nonbond_params ] section however it is
>>>not
>>> exist in ffnonbonded.itp?
>>> Any help would be appreciated.
>>>
>>> Thanks in advance.
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive
On 6/21/17 7:11 AM, Diez Fernandez, Amanda wrote:
Hi all,
I am running a simulation and I find that the output coordinates of the
simulation stored in “final_coordinates.gro” are distinctively different to any
of the frames from “trajectory.gro” which I obtain from :
trjconv –s file.tpr –f
Hi all,
I am running a simulation and I find that the output coordinates of the
simulation stored in “final_coordinates.gro” are distinctively different to any
of the frames from “trajectory.gro” which I obtain from :
trjconv –s file.tpr –f trajectory.xtc –o trajectory.gro
When I visualise
