I agree with Ross here ...
Vlad
On May 18, 2015 6:07:07 PM CEST, Ross Walker <ross.rosswalker.co.uk> wrote:
>This is mostly moot since 'reproducibility' means being able to
>reproduce someone's conclusions and not their specific results.
>Something that a lot of funding agencies don't seem to understand when
>they talk about reproducibility and making data available etc etc. But
>my reading of the text in the paper
>
>>>>>>>> "380 ps initial MD run with consecutively weaker restraints on
>>>>>>>> protein atoms and gradually heat up the system to 300K"
>
>is that they likely just ran 20ps with restraint blah, then another
>20ps with restrain blah*0.x then another 20ps with blahx0.y etc etc. I
>don't see anything in that wording which refers to the term 'steadily'
>or 'linearly' decreasing restraints. I'd look in the supplemental
>material to figure out what they actually did - if it is not there then
>that is a little sloppy in terms of specifying the methodology used
>etc.
>
>At the end of the day though, who the hell cares. If you have to
>reproduce their protocol exactly to reproduce their conclusions then
>the conclusions are worthless.
>
>All the best
>Ross
>
>>
>> On 05/18/2015 04:13 PM, Juan Eiros Zamora wrote:
>>> Hi all,
>>>
>>> I'm aware that even if I do exactly the same preparation of the
>system I
>>> will get differences on the results, as that is the nature of MD,
>but
>>> all in all the conclusions of the study should be the same.
>>>
>>> I would ask for the scripts but the issue is that they used NAMD
>instead
>>> of AMBER. Is there a way to use NAMD input files with AMBER? Or am I
>>> just being silly here?
>>>
>>> Anyway thanks for the suggestions, for the moment I think I'll just
>do
>>> it sequentially.
>>>
>>> Cheers,
>>>
>>> Juan
>>>
>>> On 18/05/15 15:00, Vlad Cojocaru wrote:
>>>> Sure ... Hannes is also right. Even if you apply the same protocol
>is
>>>> unlikely you'll get exactly the same results ... However, if you
>are
>>>> after reproducing the overall conclusions of a study, they should
>be
>>>> protocol-independent provided a protocol does not introduce
>artefactual
>>>> behavior. So, probably in this case the best bet is to get the
>original
>>>> scripts for the published protocols from the authors.
>>>>
>>>> Hope this helps a bit
>>>> Vlad
>>>>
>>>> On 05/18/2015 03:56 PM, Vlad Cojocaru wrote:
>>>>> Dear Juan,
>>>>>
>>>>> Probably the best way to reproduce published data is to ask the
>authors
>>>>> for the protocols ..
>>>>>
>>>>> Best
>>>>> Vlad
>>>>>
>>>>>
>>>>> On 05/18/2015 03:37 PM, Juan Eiros Zamora wrote:
>>>>>> Hi Hannes,
>>>>>>
>>>>>> It's just that I'm trying to replicate the MD protocol of a
>paper, but
>>>>>> the authors used NAMD 2.9, and they stated in their Materials and
>>>>>> Methods that they heat up the system and change the constraints
>at the
>>>>>> same time. So I'm trying to introduce the least changes as
>possible in
>>>>>> order to obtain similar results to them.
>>>>>>
>>>>>> But if it's not possible in AMBER then I will just do it
>sequentially as
>>>>>> you suggested.
>>>>>>
>>>>>> Thanks for your input,
>>>>>>
>>>>>> Juan
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 18/05/15 13:13, Hannes Loeffler wrote:
>>>>>>> Hi,
>>>>>>>
>>>>>>> I am not aware that you could change the restraint force during
>MD so I
>>>>>>> think you would have to emulate that through several steps.
>Possibly
>>>>>>> script this.
>>>>>>>
>>>>>>> Why is it important to you to do the heating and restraint
>release at
>>>>>>> the same time? What's wrong with doing this step-wise?
>>>>>>>
>>>>>>> Cheers,
>>>>>>> Hannes.
>>>>>>>
>>>>>>>
>>>>>>> On Mon, 18 May 2015 13:06:56 +0100
>>>>>>> Juan Eiros Zamora <j.eiros-zamora14.imperial.ac.uk> wrote:
>>>>>>>
>>>>>>>> Hi everyone,
>>>>>>>>
>>>>>>>> I am trying to replicate an MD protocol that has been done
>previously
>>>>>>>> using NAMD 2.9 using AMBER.
>>>>>>>>
>>>>>>>> After the initial minimisation steps (water and ions, then
>backbone
>>>>>>>> of protein and so on), I am trying to do the following:
>>>>>>>>
>>>>>>>> "380 ps initial MD run with consecutively weaker restraints on
>>>>>>>> protein atoms and gradually heat up the system to 300K"
>>>>>>>>
>>>>>>>> Usually in my minimisation input file I keep the restraints
>constant
>>>>>>>> like this:
>>>>>>>>> Stage 1 - 1000 step minimisation of water and ions
>>>>>>>>> &cntrl
>>>>>>>>> imin=1, maxcyc=1000, ncyc=500,
>>>>>>>>> cut=12.,ntb=1,ntr=1,
>>>>>>>>> ntpr=100
>>>>>>>>> /
>>>>>>>>> Hold protein fixed
>>>>>>>>> 500.0
>>>>>>>>> RES 1 422
>>>>>>>>> END
>>>>>>>>> END
>>>>>>>> And to heat up a system I do it like this (after the &cntrl
>section):
>>>>>>>>
>>>>>>>>> &wt type='TEMP0', istep1=0, istep2=50000,
>>>>>>>>> value1=0.0, value2=300.0 /
>>>>>>>>> &wt type='END' /
>>>>>>>>> Hold protein fixed
>>>>>>>>> 10.0
>>>>>>>>> RES 1 422
>>>>>>>>> END
>>>>>>>>> END
>>>>>>>> Does anyone have an idea of how could I change two variables at
>a
>>>>>>>> time? I've looked into section 18.8 of the Manual, but I am not
>sure
>>>>>>>> if I should change the BOND option or the REST one, or how to
>proceed
>>>>>>>> to change one of the two as well as the TEMP0 option.
>>>>>>>>
>>>>>>>> Looking forward to hear any suggestion on this matter,
>>>>>>>>
>>>>>>>> Juan
>>>>>>>>
>>>>>>>>
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>>>>>>
>>>
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>>
>> --
>> Dr. Vlad Cojocaru
>> Computational Structural Biology Laboratory
>> Department of Cell and Developmental Biology
>> Max Planck Institute for Molecular Biomedicine
>> Röntgenstrasse 20, 48149 Münster, Germany
>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>> http://www.mpi-muenster.mpg.de/43241/cojocaru
>>
>>
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Received on Mon May 18 2015 - 11:00:03 PDT
