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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>>
--
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 - 07:30:03 PDT
