Re: [AMBER] How to remove PBC effects?

From: Oliver Kuhn <>
Date: Mon, 19 Jul 2010 15:55:31 +0200 (CEST)

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.

> 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
>On Mon, Jul 19, 2010 at 9:04 PM, Oliver Kuhn <> 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 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 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
Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief!
Jetzt De-Mail-Adresse reservieren:

AMBER mailing list
Received on Mon Jul 19 2010 - 07:00:03 PDT
Custom Search