AMBER Archive (2009)

Subject: Re: [AMBER] equilibration stops for dimer simulation with REMD

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sun May 03 2009 - 06:11:07 CDT

it's not possible to help without more information on "simulation stops". is
there an error message, either in the sander output or output from any
queueing software? does the simulation stop, or keep running but not produce
output? does a non-REMD (normal MD) simulation work fine for the dimer using
exactly the same input but not exchanging?

On Sat, May 2, 2009 at 4:11 PM, Sunita Patel <sunita_iitb_at_yahoo.com> wrote:

> Dear Users,
>
> I am trying to simulate a dimer using implicit solvent model
> (generalized-Born solvation model) with replica exchange molecular dynamics
> at 16 different replicas. I am using AMBER10. The total number of atoms of
> the system are 4135. I set up the system for 200 ps equilibration at
> different replica temperatures after the minimization. The equilibration
> stops after completing 40ps. However, for the monomer of the same protein,
> it works fine without any problem.
>
> Could anyboby suggest what would be the problem ? When I saw the 40ps
> equilibration trajectory in VMD I didn't see anything wrong in the
> structure. The dimer structure is intact.
>
> Your suggestion will be highly appreciated.
> Thanks.
> -Sunita
>
>
>
>
>
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