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 - 12:32:42 CDT

I don't think that's the cause of the problem. 10.2 for restraint energy
seems fine if it is multiple restraints.

On Tue, May 5, 2009 at 1:26 PM, Sunita Patel <sunita_iitb_at_yahoo.com> wrote:

> Dear Users,
>
> I looked the out file from all replicas and in one replica there was a
> problem pasted below. It looks like the chiral constrain I set with the
> molecular is causing the problem and thus SHAKE fails to change the
> coordinates. I am again trying a simulation without any restrain let see...
>
> ----------------
> NSTEP = 20000 TIME(PS) = 40.000 TEMP(K) = 327.42 PRESS =
> 0.0
> Etot = -2148.8682 EKtot = 3357.6998 EPtot =
> -5506.5680
> BOND = 885.1275 ANGLE = 2238.7037 DIHED =
> 2623.0592
> 1-4 NB = 850.0974 1-4 EEL = 11564.6743 VDWAALS =
> -1647.4948
> EELEC = -17552.8878 EGB = -4478.0646 RESTRAINT =
> 10.2171
> EAMBER (non-restraint) = -5516.7851
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 10.217
>
> ===============================================================================
> vlimit exceeded for step 20072; vmax = 23.7610
> vlimit exceeded for step 20073; vmax = 22.6276
> vlimit exceeded for step 20074; vmax = 228.1686
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 0 1193 2374 2375
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
> ---------------
> Thank you guys.
> Sunita
>
>
> --- On Tue, 5/5/09, 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: Tuesday, May 5, 2009, 10:03 PM
>
> 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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