Thank you Anselm and Jason. I'm going to check Jason suggestion as I'm
not very sure about the consequences of fixing an atom coordinates.
Best regards,
Fernando
On Wed, 8 Aug 2012 08:09:53 -0400, Jason Swails wrote:
> IMO, a better solution would be to use cpptraj and the "autoimage"
> function
> (make sure you have up to AmberTools bugfix.19 applied -- you can
> check
> this via $AMBERHOME/patch_amber.py --patch-level) on the troublesome
> restart file. This will move your protein back to the center of the
> box
> and re-image your solvent and other small molecules around it.
>
> It should also keep velocities intact, so you should be able to
> continue MD
> from there without any issues.
>
> HTH,
> Jason
>
> On Wed, Aug 8, 2012 at 7:27 AM, Anselm Horn <
> Anselm.Horn.biochem.uni-erlangen.de> wrote:
>
>> Hi Fernando,
>>
>> maybe fixing one of the respective atoms to its position with
>> harmonical
>> restraints would be an option. With this you'd prevent your
>> molecule, or
>> at least the interesting part, from leaving your box.
>>
>> However, I've never done this and am not sure whether this
>> introduces
>> too much perturbation on your system.
>>
>> Regards,
>>
>> Anselm
>>
>> Bioinformatik
>> Institut für Biochemie
>> Friedrich-Alexander-Universität Erlangen-Nürnberg
>> Germany
>>
>> Am 08.08.2012 12:35, schrieb Fernando Martín García:
>> > But, if I understood well, iwrap doesn't resolve the high
>> diffusion of
>> > the protein in the box (and I proved with iwrap=1 too). So, the
>> only
>> > solution is to enlarge the box size? Is there any other
>> possibility?
>> >
>> > Thanks,
>> >
>> > Fernando
>> >
>> > On Wed, 8 Aug 2012 12:13:51 +0200, Jérôme Golebiowski wrote:
>> >> If you are performing an umbrella sampling and this extends your
>> >> molecule to
>> >> larger value than your box size, you should enlarge your box.
>> >> Otherwise, maybe just setting iwrap to 1 will help keeping the
>> >> protein close to
>> >> the box center.
>> >> HTH.
>> >> Best,
>> >> Jerome
>> >>
>> >>
>> >>
>> >> Selon Fernando MartÃn GarcÃa <fmgarcia.cbm.uam.es>:
>> >>
>> >>> Dear Amber users,
>> >>>
>> >>> I have a "technical" problem with a distance restraint. I'm
>> working
>> >>> with a protein with a 12 angs. TIP3 box. The simulation time
>> is 30
>> >>> ns.
>> >>> After 20 ns, a small part of the protein is out of the box.
>> The
>> >>> problem
>> >>> is that one of the residues out of the box has a restrain with
>> one
>> >>> residue in the part of the protein inside the water box, so
>> the
>> >>> value
>> >>> changes, what it causes a high restraint value. Is there any
>> >>> solution
>> >>> for this?
>> >>>
>> >>> Thanks
>> >>> --
>> >>> ==============================================
>> >>> Fernando MartÃn GarcÃa
>> >>> Molecular Modelling Group - Lab 312.1
>> >>> Molecular Biology Center "Severo Ochoa"
>> >>> C/ NICOLáS CABRERA, 5.
>> >>> UAM University. Cantoblanco, 28049 Madrid. Spain.
>> >>> TEL: (+34) 91-196-4662 FAX: (+34) 91-196-4420
>> >>> Web: http://fertoledo.wordpress.com/
>> >>> ==============================================
>> >>>
>> >>> _______________________________________________
>> >>> AMBER mailing list
>> >>> AMBER.ambermd.org
>> >>> http://lists.ambermd.org/mailman/listinfo/amber
>> >>>
>> >>>
>> >>
>> >>
>> >> --
>> >> Jérôme Golebiowski
>> >> Institute of Chemistry - Nice
>> >> Molecular Modeling Team
>> >> UMR 7272 CNRS, University of Nice Sophia Antipolis
>> >> 06108 Nice cedex 2, France
>> >>
>> >> tel: +33 (0)4 92 07 61 03
>> >> http://www.unice.fr/icn
>> >> http://www.unice.fr/icn/golebiowski
>> >>
>> >> _______________________________________________
>> >> 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
>>
--
==============================================
Fernando Martín García
Molecular Modelling Group - Lab 312.1
Molecular Biology Center "Severo Ochoa"
C/ NICOLáS CABRERA, 5.
UAM University. Cantoblanco, 28049 Madrid. Spain.
TEL: (+34) 91-196-4662 FAX: (+34) 91-196-4420
Web: http://fertoledo.wordpress.com/
==============================================
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 08 2012 - 05:30:03 PDT
