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
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 18 2015 - 07:00:06 PDT
