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
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Received on Wed Sep 16 2020 - 08:30:03 PDT
