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

Mark Abraham mark.j.abraham at gmail.com
Tue Dec 24 00:31:59 CET 2013 

On Mon, Dec 23, 2013 at 8:43 PM, Rasoul Nasiri <nasiri1355 at gmail.com> wrote:

> Thanks for your replies.
>
> 1- I need bond and charge info along with position and velocity ones.
> All change during the MD simulation required a reactive force field rather
> than
> traditional one.
>
> 2- How one can construct a tpr for a system in which bonds/charges change
> when it's evolved?
>

You can't make a proper .tpr, because the general assumption is that
connectivity and charge are within the MM approximation, i.e. constant. You
can certainly make one that matches a given configuration, but you'll need
to get your hands dirty with a script that can assign (say) partly-formed
bonds to be one or the other thing.

Mark


> Best,
> Rasoul
>
>
> On Mon, Dec 23, 2013 at 9:30 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
>
> > 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
> > > > > > --
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> > > > > --
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