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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Received on Mon May 18 2015 - 07:30:06 PDT
