Re: [AMBER] error

From: James Kress <>
Date: Wed, 11 Dec 2019 12:36:15 -0500

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?


James Kress Ph.D., President
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-----Original Message-----
From: David A Case <>
Sent: Wednesday, December 11, 2019 11:41 AM
To: AMBER Mailing List <>
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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