The easiest way and the most trustable way is look at both files.
See if the last serveral coordinations in your mdcrd file match the
corresponding coordinations in your restart file.
Mingfeng
Lishan Yao wrote:
>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.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.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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Received on Thu Oct 27 2005 - 20:53:02 PDT
