AMBER Archive (2009)

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

From: Sunita Patel (sunita_iitb_at_yahoo.com)
Date: Sun May 03 2009 - 20:30:05 CDT

Hi Carlos,

Thanks for your reply.
The equilibration didn't give any error message in the out file. However, the queuing software gave the following output.
--------------------------------------------------------
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 12[cli_12]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 12
-------------------------------------------------------
The last step of the out file after which equilibration stopped is also given below.
=======================================

NSTEP =    19500   TIME(PS) =      39.000  TEMP(K) =   282.09  PRESS =     0.0
 Etot   =     -3118.8017  EKtot   =      2892.7694  EPtot      =     -6011.5711
 BOND   =       764.7012  ANGLE   =      1948.1010  DIHED      =      2561.2296
 1-4 NB =       844.0953  1-4 EEL =     11622.4414  VDWAALS    =     -1680.7828
 EELEC  =    -17555.6673  EGB     =     -4523.3717  RESTRAINT  =         7.6822
 EAMBER (non-restraint)  =     -6019.2533
 ------------------------------------------------------------------------------

The parameter file for equilibration step is also appended here.

Equilibration
 &cntrl
   irest=0, ntx=1,
   nstlim=100000, dt=0.002,
   ntt=3, gamma_ln=1.0,
   temp0=281.85, ig=13004,
   ntc=2, ntf=2, nscm=1000,
   ntb=0, igb=5,
   cut=16.0, rgbmax=16.0,
   ntpr=500, ntwx=500, ntwr=100000,
   nmropt=1,
 /
 &wt TYPE='END'
 /
DISANG=dimer_chir.dat
-------------------------------------------------------------------------

I hope, this information would help you to figure out the problem. I have not done none REMD simulation on this system. As you suggested I will give a try to do normal MD and see.

Thank you so much.
Regards,
Sunita

--- On Sun, 5/3/09, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:

From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
Subject: Re: [AMBER] equilibration stops for dimer simulation with REMD
To: "AMBER Mailing List" <amber_at_ambermd.org>
Date: Sunday, May 3, 2009, 4:41 PM

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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