I think Dave's point was about format, not really content of the file.
restart and trajectory files can have different formats. In regard to your
question, a restart file generated from the MD program should have
velocities. A "restart" formatted coordinate file extracted from a
trajectory may not have velocities, depending on how it is constructed and
if velocities were available. The MD program can assign velocities in such
cases.
On Wed, Dec 11, 2019 at 12:36 PM James Kress <jimkress_58.kressworks.org>
wrote:
> Is there any particular reason the restart files do not contain velocities?
> It seems to me that a "true restart" would need to have coordinates and
> velocities to accurately continue an interrupted run?
>
> What am I not understanding?
>
> Jim
>
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> -----Original Message-----
> From: David A Case <david.case.rutgers.edu>
> Sent: Wednesday, December 11, 2019 11:41 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] error
>
> On Wed, Dec 11, 2019, MYRIAN TORRES RICO wrote:
> >
> >Exactly, I want to run pmemd using final trayectory (.mdcrd) instead
> >firsts coordinates (.crd).
>
> You can't do this (directly): trajectory files have lots of coordinates
> (frames) in them, whereas a restart file has only one set of coordinates.
> pmemd doesn't know how to start from a trajectory file.
>
> Do you have a "final" restart file (created with the "-r" flag)? Might
> that
> not be what you want here, as a starting point for the next MD segment?
>
> If not, do this: use cpptraj, with trajin being the trajectory file:
> choose the frame you wish to use. Set trajout to write a restart file.
>
> Then you can use the restart file you just created. It won't have any
> velocities, so you will have to set ntx=1 and tempi to the initial
> temperature you want.
>
> ....hope this helps....dac
>
>
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Received on Wed Dec 11 2019 - 11:30:01 PST
