Have a look at the attach pull release tutorial on the amber site
Von meinem iPad gesendet
> Am 13.04.2017 um 15:04 schrieb Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>:
>
> On Thu, 13 Apr 2017 09:27:20 +0000
> 吴萌 <wumeng.shanghaitech.edu.cn> wrote:
>
>> Dear All,
>>
>> I am trying to use the AMBER umbrella sampling method to get the
>> free energy of transfer profile for a substrate molecule through a
>> channel protein. And I have referred
>> https://github.com/callumjd/AMBER-Umbrella_COM_restraint_tutorial ,
>> but several problems have trapped me due to my system is different.
>>
>> 1) If I put one substrate molecule close to the protein channel
>> entrance, how can I define its location, I mean such as Z=0(need it
>> to get r2=? in the pull.RST)
>
> It looks like you are defining a distance between the groups igr1 and
> igr2 so I would think that you set r2 to the current distance.
>
>
>> 2) Also the distance restraint file, I
>> use igr1=substrate atom number, how should I difine igr2=? use
>> residue near the protein channel exit? If yes, use one or several?
>
> The tutorial you refer to uses the center-of-mass (COM) of all head
> groups which probably, on average, means in the center of the box with
> respect to the x and y distance (or bilayer actually if it is the head
> groups of both leaves). The tutorial only considers the distance between
> the bulk and the center of the bilayer as the order parameter (and so
> assumes symmetry).
>
> I suspect the COM of each group will only be computed once at the
> beginning of the simulation. What I would do is to introduce a
> virtual/dummy atom at a convenient location (maybe use ibelly to fix
> it in space) and use that as reference point.
>
> Plumed would allow you to conveniently do all this but this is only
> available for sander. There is some similar functionality (US, SMD) in
> the NFE code (previously known as NCSU) but I can't see in the manual
> that you could define virtual sites or consider only one specific
> component of the cartesian coordinate.
>
> Cheers,
> Hannes.
>
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Received on Thu Apr 13 2017 - 10:00:04 PDT
