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

[Tsjerk Wassenaar]

Also, consider what you need it for. If you only need atom/residue
information and/or reference coordinates, a .gro/.pdb file will do. Only if
you need to have bonds/masses/charges/... you really need a .tpr file for
reference.

Cheers,

Tsjerk


On Mon, Dec 23, 2013 at 4:00 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> 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
> > > > --
> > > > Gromacs Users mailing list
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> > >
> > >
> > >
> > > --
> > > Tsjerk A. Wassenaar, Ph.D.
> > > --
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-- 
Tsjerk A. Wassenaar, Ph.D.