Re: [AMBER] How to remove PBC effects?

From: Oliver Kuhn <oak.amber.web.de>
Date: Tue, 20 Jul 2010 10:36:10 +0200 (CEST)

-----Urspr√ľngliche Nachricht-----
Von: Jason Swails <jason.swails.gmail.com>
Gesendet: 19.07.2010 17:08:07
An: AMBER Mailing List <amber.ambermd.org>
Betreff: Re: [AMBER] How to remove PBC effects?

>Hi Oliver,
>
>This isn't a COM translation problem. Keep in mind that a simulation has no
>idea of the distinction between solvent and solute when it comes to
>determining center of mass, so while dan was right and ncsm performs as he
>described, that will not prevent your complex from splitting apart.
>
>The reason this is actually happening is due to your use of iwrap. One
>monomer is getting wrapped to the other side of the periodic box when it
>comes too close to the edge of the box. The solution in my experience is to
>center and image once for each individual species that is in your system.
>In the case of a non-bonded dimer with a ligand, that is 3x. The first is
>the first monomer, the second is both monomers, and the 3rd is both monomers
>and the ligand. This should put everything back into the same box (and you
>might as well strip waters and ions and use "strip_mdcrd=0" in your
>MMPBSA.py input file).
>
>Hope this helps,
>Jason

Eventually, I got it ;)
Thanks Jason.

>
>On Mon, Jul 19, 2010 at 9:55 AM, Oliver Kuhn <oak.amber.web.de> wrote:
>
>> Thanks Dan,
>> I'm very much worried about that being the only solutions because I have
>> already dozens of 4-10ns simulations on which I want to do binding affinity
>> calculations.
>> I hope that it is also possible to transform these trajectories into such
>> that can be used as input for MMPBSA.
>>
>>
>> >Oliver,
>> > Is it a problem with the COM motion? If so, you can simply set the
>> nscm=10
>> >(default 1000)
>> >or some other small number (much smaller than your COM diffusion rate I
>> >would guess).
>> >This will reset the center of mass to the origin every nscm steps.
>> >I think this corresponds to your possibility #1. To me this is the easiest
>> >solution.
>> >--Dan
>> >
>> >On Mon, Jul 19, 2010 at 9:04 PM, Oliver Kuhn <oak.amber.web.de> wrote:
>> >
>> >> Dear Amber Users and Developers,
>> >> I'm still having trouble with a well know issue: A dimeric protein
>> diffuses
>> >> across the periodic boundary and is split into monomers (as can be seen
>> in
>> >> the attached png).
>> >> The trajectory is needed for a MMPBSA.py calculation.
>> >>
>> >> I know several possibilities to circumvent this issue in principle but
>> none
>> >> works.
>> >>
>> >> 1. The center-of-mass motion should be removed by default so that the
>> >> protein stays in the box center - please correct me if I'm wrong.
>> >> (Or do I have to remove comm more often than default?)
>> >>
>> >> 2. iwrap=1 should map all atoms into the primary box when writing the
>> >> trajectory.
>> >>
>> >> 3. tleap can be used to map the atoms back into the primary box - this
>> is
>> >> somewhat tricky (by centering two times - on time without and then with
>> >> ligand) implemented in the MMPBSA.py script:
>> >> trajin production.mdcrd 1 1000 1
>> >> strip :WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+
>> >> center :1-198 mass origin
>> >> image origin center
>> >> center :1-199 mass origin
>> >> image origin center
>> >> rms first mass :1-198
>> >> average _MMPBSA_avgcomplex.pdb pdb
>> >> trajout _MMPBSA_complex.mdcrd nobox
>> >>
>> >> In the end, I still run into problems with my energy calculations (as
>> can
>> >> be seen in the attached pdf - 20 simulations with 3 of them having PBC
>> >> effects).
>> >> Can anybody tell me how to prepare the trajectories so that monomer1,
>> >> monomer2 and ligand coordinates are in one box?
>> >>
>> >> Thanks for any help
>> >> Oliver
>> >--
>> >Dr. Daniel J. Sindhikara
>> >Institute for Molecular Science
>> >E-mail: sindhikara.gmail.com
>> >Website: http://sites.google.com/site/dansindhikara/
>> >--
>> ___________________________________________________________
>> Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief!
>> Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
>--
>Jason M. Swails
>Quantum Theory Project,
>University of Florida
>Ph.D. Graduate Student
>352-392-4032
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
___________________________________________________________
Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief!
Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 20 2010 - 02:00:03 PDT
Custom Search