[gmx-users] conversion of X,Y,Z + velocities to *.trr

[Mark Abraham]

Hi,

Constructing a .tpr is covered many GROMACS tutorials you can find. What is
particular about your case that you do not have one from doing the
simulation?

Mark


On Mon, Dec 23, 2013 at 9:40 AM, Rasoul Nasiri <nasiri1355 at gmail.com> wrote:

> Many thanks Tsjerk,
>
> Let me ask another question. As you know in most cases of analysis, one
> needs to have tpr file along with the trajectory.
> How can I construct it? The potential that I'm using in my MD simulations
> is ReaxFF (a reactive FF).
>
> Best,
> Rasoul
>
>
> On Sun, Dec 22, 2013 at 9:21 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
>
> > Hi Raoul,
> >
> > You can also convert it to .gro or .pdb and do the analysis on that.
> > Scriptwise that's trivial.
> >
> > Cheers,
> >
> > Tsjerk
> >
> >
> > On Sat, Dec 21, 2013 at 10:12 PM, Rasoul Nasiri <nasiri1355 at gmail.com
> > >wrote:
> >
> > > Dear all,
> > >
> > > Is there any available script/Tcl in order to convert a x,y,z
> trajectory
> > > (x,y,z-coordinates+velocities) to *.trr one?
> > >
> > > I have optained the following trajectory and I need to have *.trr for
> > > analysing of my MD;
> > >
> > >
> > > C   45.96903  21.49863  24.62913        0.00000        0.00000
> > > 0.00000
> > > H   47.06603  21.49863  24.62913        0.00000        0.00000
> > > 0.00000
> > > H   45.80503  22.58663  24.62913        0.00000        0.00000
> > > 0.00000
> > > H   45.56903  21.09663  25.55113        0.00000        0.00000
> > > 0.00000
> > > C   45.38203  20.69563  23.47013        0.00000        0.00000
> > > 0.00000
> > > H   45.90103  19.74763  23.37813        0.00000        0.00000
> > > 0.00000
> > > H   45.64903  21.18663  22.53113        0.00000        0.00000
> > > 0.00000
> > > C   43.87003  20.45463  23.58413        0.00000        0.00000
> > > 0.00000
> > > .
> > > .
> > > .
> > > .
> > >
> > > Any help is highly appreciated.
> > >
> > > Best,
> > > Rasoul
> > > --
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> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
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