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
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--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
--
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Received on Mon Jul 19 2010 - 06:30:03 PDT
