Actually you are right, it is much easier -and technically correct- to
enlarge the box rather than doing all these alchemies I described to
prevent periodic contacts. I just wanted to avoid equilibrating and
recalculating boost parameters for aMD, but it seems inevitable.
Just for the record, I would like to know if applying a force along an axis
without modifying the code is possible?
thanks,
Thomas
On 28 January 2013 12:56, Thomas Evangelidis <tevang3.gmail.com> wrote:
> Daniel and Ross,
>
> I was just asking if there is a way to find atoms from periodic images
> within a given cutoff of an atom in the primary cell, something like the
> "pbwithin" macro of VMD.
>
> I carefully decided the box dimensions to avoid such effects. The protein
> C-teminus was pinned down with coordinate restraints to eliminate diffusion
> and use a smaller box, as I am only interested in the dynamics o the
> N-terminus. It appears that I have set the Z-dimension a few Angstroms
> shorter than it should be. In my opinion, that periodic contact resulted
> from an unnatural stretch on the folded part of the protein and a
> concurrent unfolding of the flexible N-terminus that was driven by its high
> positive charge and perhaps the ions (I use a NaCl concentration of 0.15
> mM) that bridge the positive N-term with the negative C-term on the
> periodic cell. Since the simulation has progressed too much, I would prefer
> to give a flick to the N-term so that it goes away from that position and
> let the molecule adopt a "more natural" conformation. And of course I will
> not include that part of the trajectory in my analysis.
>
> Is it possible to apply a force along the Z-axis with NMR-based
> restraints? I have found an older post in the list which says that
> modification to the code must be made.
>
> thanks,
> Thomas
>
>
>
>
> On 28 January 2013 03:07, Ross Walker <ross.rosswalker.co.uk> wrote:
>
>> Hi Thomas,
>>
>>
>> This is not possible in AMBER and even if it was I do not believe that it
>> will do what you actually think it will do. Any restraint to an image can
>> be recast as an internal restraint, since you have periodic boundaries and
>> cannot be anything other than this. Placing a minimum distance restraint
>> between the C terminal of your protein and the N terminal of an image is
>> exactly the same as placing the same restraint between the two ends of the
>> central protein with the distance and sign of the force constant just
>> adjusted for the imaging. In effect all you will actually do is squash the
>> two ends of your protein together compacting it which is what you
>> definitely don't want to do. Ultimately you need to make the size of your
>> solute box larger to avoid such periodic artifacts.
>>
>> All the best
>> Ross
>>
>> On 1/27/13 10:22 AM, "Thomas Evangelidis" <tevang3.gmail.com> wrote:
>>
>> >Dear AMBER users,
>> >
>> >I would like to know if distance restraints between the protein in the
>> >primary cell and one of its periodic images are allowed. The C-terminal
>> >loop of my protein interacts at some point of the simulation with the
>> >N-terminus of the protein in a periodic cell, and stays there for a long
>> >time. To avoid that I would like to apply a force that moves away the
>> >C-terminal loop whenever it reaching a cutoff distance from the periodic
>> >image. Is this possible in AMBER?
>> >
>> >
>> >thanks,
>> >Thomas
>> >
>> >
>> >--
>> >
>> >======================================================================
>> >
>> >Thomas Evangelidis
>> >
>> >PhD student
>> >University of Athens
>> >Faculty of Pharmacy
>> >Department of Pharmaceutical Chemistry
>> >Panepistimioupoli-Zografou
>> >157 71 Athens
>> >GREECE
>> >
>> >email: tevang.pharm.uoa.gr
>> >
>> > tevang3.gmail.com
>> >
>> >
>> >website: https://sites.google.com/site/thomasevangelidishomepage/
>> >_______________________________________________
>> >AMBER mailing list
>> >AMBER.ambermd.org
>> >http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: tevang.pharm.uoa.gr
>
> tevang3.gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
>
>
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Wed Jan 30 2013 - 09:00:02 PST
