AMBER Archive (2005)

Subject: Re: AMBER: restart file and crd file

From: Lishan Yao (yaolisha_at_msu.edu)
Date: Thu Oct 27 2005 - 12:54:26 CDT

But the total steps are 500,000. The last snapshot should be the same as
restart, right?

Lishan

On Thu, 2005-10-27 at 15:03, Carlos Simmerling wrote:
> if you write the traj file every 1000 steps and restarts every 100 steps,
> they will not match.
>
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
> Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
> ===================================================================
>
>
>
>
> Lishan Yao wrote:
>
> >The simulation finishes normally. The restart file was written out by
> >default, every 100 steps.
> >
> >Best,
> >Lishan
> >
> >On Thu, 2005-10-27 at 12:18, Carlos Simmerling wrote:
> >
> >
> >>did the simulation finish normally? how often did you write
> >>restarts?
> >>
> >>===================================================================
> >>Carlos L. Simmerling, Ph.D.
> >>Associate Professor Phone: (631) 632-1336
> >>Center for Structural Biology Fax: (631) 632-1555
> >>Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
> >>Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
> >>===================================================================
> >>
> >>
> >>
> >>
> >>Lishan Yao wrote:
> >>
> >>
> >>
> >>>Dear Amber users:
> >>> I did a 500,000 steps MD simulation and I saved snapshots every 1000
> >>>steps. My question is whether the restart file and the last snapshot in
> >>>crd (trajectory) file has the same structure? The reason I ask this
> >>>question is that I found out water molecules in active site have
> >>>different positions in the two structures.
> >>>
> >>> Thank you in advance.
> >>>
> >>>Best,
> >>>Lishan
> >>>
> >>>
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> >
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