AMBER Archive (2005)

Subject: Re: AMBER: restart file and crd file

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Thu Oct 27 2005 - 11:18:18 CDT

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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