Hello,
David's advice is correct, but there's a small detail missing here.
I'm guessing that you did not save velocities (i.e. in a mdvel file) during
your simulation, so your restart file will not be a complete restart file.
All of the velocities will be zeroed, so you'll either have to re-heat your
system are assign a random M-B weighted velocity distribution; in either
case it won't be a true restart (ignoring the fact that normal restart files
have truncated precision which makes a restarted trajectory diverge from a
continuous trajectory after a small period of time).
If you didn't save these velocities, there's no way of getting them back.
Moreover, since you most likely didn't save trajectory snapshots every step,
it'll be impossible to calculate the velocities with any kind of
finite-difference differentiation using the snapshots.
Hope this helps,
Jason
On Fri, Mar 11, 2011 at 9:14 AM, david condon <dec986.gmail.com> wrote:
> Hi Rahul,
>
> trajin works by "trajin filename [ start stop offset]", according to
> the Amber9 manual, p. 246. Trajout works by "trajout filename [
> format ]" also from Amber manual.
>
> 2000 is the frame number. I save the trajectory file every 0.1 ns, so
> frame 2000 would represent 200 ns in the trajectory.
>
> You only want to use a single frame because you are creating a restart
> file, so if you are extracting frame 1701, you would use
>
> trajin trajectory.mdcrd 1701 1701 1
> trajout restart.rst restart
>
> -Dave
>
> On 3/11/11, Rahul Banerjee <rahul.banerjee.chemistry.msu.edu> wrote:
> > Thanks Dave.
> >
> > But why do you mention "2000" twice in the trajin line? What does it
> mean?
> >
> > With best regards,
> > Rahul
> >
> > ________________________________________
> > From: david condon [dec986.gmail.com]
> > Sent: Friday, March 11, 2011 11:56 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] How to save a restart file
> >
> > Hi Rahul,
> >
> > I have done this many times with pdbs.
> >
> > You can extract it similarly to the way I do it,
> >
> > trajin ../mdall.mdcrd 2000 2000 1
> > trajout 200ns.wat.pdb pdb
> >
> > except with "restart" replacing "pdb".
> >
> > -Dave
> >
> >
> > On 3/11/11, Rahul Banerjee <rahul.banerjee.chemistry.msu.edu> wrote:
> >> Dear Amber users,
> >>
> >> I have a long trajectory for a peptide simulation using Amber. How can I
> >> save a particular snapshot (lets say nth snapshot) from the mdcrd file
> as
> >> a
> >> restart (rst) file. I want to start another simulation from the new
> >> restart
> >> file.
> >>
> >> Thank you for your comments and suggestions.
> >>
> >> With best regards,
> >> Rahul
> >>
> >> _______________________________________________
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> >>
> >
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Mar 11 2011 - 10:00:07 PST
