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 - 14:03:13 CDT


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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