When minimizing, there are no velocities.
Bill
On 12/11/19 9:36 AM, James Kress 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 - 15:00:02 PST
