This worked perfectly - thank you very much for the quick response!
Alysia
On Wed, Sep 16, 2020 at 11:06 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> So you can use cpptraj to extract the final frame of your trajectory
> and use it as a restart like so:
>
> parm file.prmtop
> trajin file.mdcrd lastframe
> trajout file.rst7
>
> Be aware though this isn't "true" restart, since velocity information
> will be missing. You can use cpptraj to set velocities from a
> Maxwell-Boltzmann distribution with the 'setvelocity' command - again
> this won't be a "true" restart but should be OK, especially if your
> total simulation time is large enough. The advantage of using cpptraj
> to do this instead of sander/pmemd is that currently the latter two
> won't correct for constrained atoms. For example:
>
> parm file.prmtop
> trajin file.mdcrd lastframe
> setvelocity tempi <T> ntc 2 zeromomentum
> trajout file.rst7
>
> Replace <T> with your target temperature. The 'ntc 2' argument has the
> same meaning as sander/pmemd, and specifies bonds to H are constrained
> (likely what you are doing). The 'zeromomentum' keyword just ensures
> that the total momentum of the system is zero. Hope this helps,
>
> -Dan
>
> On Wed, Sep 16, 2020 at 9:55 AM Alysia Mandato <alysiamandato.gmail.com>
> wrote:
> >
> > Hello!
> >
> >
> >
> > My computer broke last week and I lost a lot of data including my .rst
> > files for my simulations. I saved the .prmtop and .mdcrd files to an
> > external drive, so I have all of those. I need to continue the simulation
> > for another 1 us, but I do not have the restart file that I would
> normally
> > use to do this. Is there any way to generate a .rst from coordinate file?
> >
> >
> >
> > I tried using cpptraj:
> >
> > parm file.prmtop
> >
> > trajin file.mdcrd ß this file has 24217 frames
> >
> > trajout file.rst restart 24217
> >
> > go
> >
> > quit
> >
> > This generated 24217 individual files in this format: “file.rst.1,
> > file.rst.2,…”.
> >
> >
> >
> > Can I compile these individual files somehow to make one restart file? Or
> > is there a different way to generate the restart file? I realize this may
> > not be possible, but thank you for taking the time to try to help!
> >
> >
> >
> > Thank you,
> >
> > Alysia
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 17 2020 - 08:00:02 PDT
