AMBER Archive (2005)

Subject: Re: AMBER: restart file and crd file

From: Heiko Meyer (heiko.meyer_at_scai.fraunhofer.de)
Date: Fri Nov 04 2005 - 06:56:41 CST

hello amber users.

i´m having some similar problems with the mdcrd.
therefore i started a test-simulation writing out trajectory- and
restart-files every step.
but non of the restart-files matches the trajactory-files exactly.
mostly the differences
are in the 4th decimal place.
are calculations for the crd in the restart-files and the crd in the
trajectory-files done by
the same algorithm or could it be a rounding error??

greets
heiko

Carlos Simmerling wrote:

> 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_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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-- 
Heiko Meyer
Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI)
Schloss Birlinghoven
D-53754 Sankt Augustin, Germany

Phone: 	+49 - (0)2241 - 14 2574
Fax:   	+49 - (0)2241 - 14 2181
E-mail:	heiko.meyer_at_scai.fraunhofer.de
WWW:   	http://www.scai.fraunhofer.de

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