i solved the problem for myself:
the trajectory-files contain 3 decimal places only.
but now there is another question:
when new generated files have 7 decimal places...
where does the places 4-7 come from
when coordinates are generated from trajectory-file?
Heiko Meyer wrote:
> 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.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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>>>>>>
>>>>>
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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.scai.fraunhofer.de
WWW: http://www.scai.fraunhofer.de
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Received on Fri Nov 04 2005 - 16:53:01 PST
