yes, you're right, at that time they would match (but not always)
they should be written together, look at the code labelled "Step 5"
in runmd.f
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 - 21:53:00 PDT
