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 - 07:00:03 PDT
