AMBER Archive (2009)

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

From: Sunita Patel (sunita_iitb_at_yahoo.com)
Date: Thu May 07 2009 - 13:35:59 CDT

Hi Carlos,

You were right. The small amount of force should not be the cause. The actual cause finally we could find out. The problem was happening with dimer simulation and not with the monomer simulation. Amber numbers the atoms of the dimer in a continuous manner threating it as a single chain. The program which generate chiral file was taking that dimer.pdb file as input and was unable to distinguish atoms from different chains. There was a chiral constrain set on the atoms from different chains and that was the crux of the problem.

Anyway finally the problem is sorted out so, am happy.

Thank you.
Have a good day,
Sunita

--- On Tue, 5/5/09, 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: Tuesday, May 5, 2009, 11:02 PM

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
> >
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

      
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber