AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue May 05 2009 - 11:39:52 CDT

I didn't respond because you said you were going to do the non-REMD that I
suggested, so I was waiting to see if that worked.

just to make sure I understand- this is the REMD part that fails, not the
equilibration, right? It's not really clear from your emails above.

a closer test to REMD would be to do multisander MD from the same input
structures as the REMD run. set up exactly like REMD, but don't set rem or
numexchg. see if it works at all temperatures. you probably already did this
for the equilibration of the structures before REMD, but if not then do it
here. all structures shoud be equilibrated at their respective temperatures
before doing REMD.
after you try this, let us know a little more about the system, how you
build and equilibrated the structures prior to REMD, how you chose the
temperatures, and so on.

On Tue, May 5, 2009 at 12:33 PM, Sunita Patel <sunita_iitb_at_yahoo.com> wrote:

> Dear Users,
>
> I didn't get any response of my problem. I checked my dimer equilibration
> step by doing normal MD at one temperature. It worked fine. Only with
> replica exchange MD, job aborts after completing few steps as I mentioned in
> my previous email. However with monomer, REMD does not complain anything.
>
> Could anyone please suggest how can I solve it?
>
> Best regards,
> Sunita
> Dept of Biochem and Mol Biophys
> University of Arizona, AZ
>
>
> --- On Mon, 5/4/09, Sunita Patel <sunita_iitb_at_yahoo.com> wrote:
>
> From: Sunita Patel <sunita_iitb_at_yahoo.com>
> Subject: Re: [AMBER] equilibration stops for dimer simulation with REMD
> To: "AMBER Mailing List" <amber_at_ambermd.org>
> Date: Monday, May 4, 2009, 7:00 AM
>
> 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
> >
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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