Which input file you refer to ? If you mean the topology and
coordinates, see Jason's email.
If you mean the input file where you define the simulation parameters,
of course they are different between NAMD and AMBER but sure its
relatively easy to re-write an NAMD input into AMBER input as the
methods are the sameor if not similar. Maybe pressure coupling could
give you some headaches (not sure if newest AMBER supports Langevin
piston) but if the overall conclusions depend on pressure coupling, than
there is no need to reproduce the conclusions ...
Anyhow, if you really want to reproduce, you can use NAMD (its free). If
you do it in AMBER and you get different conclusions, you never know
which is right unless you have clear experimental data to compare
against ...
Vlad
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 - 08:00:03 PDT
