Re: [AMBER] Large Energy Jump in TMD simulation - Regarding

From: Fredrick Devadoss <Fredrick.Devadoss.uni-konstanz.de>
Date: Wed, 04 Apr 2012 14:39:04 +0200

Dear Carlos,

Thank you very much for your reply. Herewith I have enclosed the two mdout files for your perusal.

md1.out.gz - 1ns output file of the TMD simulation.
md3.out.gz - 3ns output file of the TMD simulation (in this file you can see the energy jump)

Expecting your reply and thanks in advance.

Warm regards
Fredrick.

[FYI: we uploaded all the files related to this TMD simulation in our homepage. Please have a look for the link in one of my earlier mails]

On Wednesday, April 4, 2012 13:55 CEST, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
 
> can you send the mdout file from the exact 1ns run that first had the
> problem?
>
> On Wed, Apr 4, 2012 at 6:09 AM, Fredrick Devadoss <
> Fredrick.Devadoss.uni-konstanz.de> wrote:
>
> > Dear Carlos,
> >
> > Two Mg ions were there in the vicinity (without much change in the
> > internal coordinates). Nothing is unusual.
> >
> > Warm regards
> > Fredrick.
> >
> >
> > On Wednesday, April 4, 2012 12:00 CEST, Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> > > does anything unusual appear in the visualization of that trajectory?
> > > particularly with the Mg ions?
> > >
> > > On Wed, Apr 4, 2012 at 5:53 AM, Fredrick Devadoss <
> > > Fredrick.Devadoss.uni-konstanz.de> wrote:
> > >
> > > > Dear Carlos,
> > > >
> > > > Thank you very much for your reply and your comments were highly
> > > > appreciated.
> > > >
> > > > Herewith I have explained you the scenario:
> > > >
> > > > Since the wall-time of the cluster where I was running this job was 24
> > > > hours, I splited the TMD input file for every nanosecond. So the third
> > > > input file is starting from 3.0 Angstrom to 2.5 Angstrom. The input
> > file I
> > > > have attached in one of my previous mail is the first input file
> > (starting
> > > > from 3.783 to 3.5 Angstrom).
> > > >
> > > > I am using TIP3P waters only. But I have 2 Mg+ ions in the tgt mask.
> > Also
> > > > few atoms are from the protein, few from the DNA in addition to the
> > above
> > > > mentioned 2 Mg+ ions, in the tgt masks. (As I mentioned earlier, the
> > system
> > > > I am using is a Protein-DNA complex with these 2 Mg+ ions).
> > > >
> > > > I really wonder, why there is an increase in the electrostatic energy,
> > > > which cause the change in the total energy, obviously, in the third
> > > > nanosecond of my TMD simulation (for the first 2ns with low energy -
> > > > [state1] - and from 4ns to 10ns with high energy -[state2]). If you
> > look
> > > > into the total energy graph (attached in the previous mail), this
> > change is
> > > > continuous and there is no sudden jump or kink in the electrostatic
> > energy
> > > > (and hence the total energy) during the 3ns of this TMD simulation. The
> > > > inputs for the TMD simulation were taken from the output of a 10ns MD
> > > > simulation (the system was minimized, equilibrated and the production
> > run
> > > > 10ns), which was carried out earlier.
> > > >
> > > > I still wonder, because of these 2 Mg+ ions in the tgt mask, will it
> > cause
> > > > 50000 kcal/mol?
> > > >
> > > > Expecting your reply and thanks in advance.
> > > >
> > > > Warm regards
> > > > Fredrick.
> > > >
> > > >
> > > >
> > > > On Tuesday, April 3, 2012 17:21 CEST, Carlos Simmerling <
> > > > carlos.simmerling.gmail.com> wrote:
> > > >
> > > > > your sander output says that the target RMSD value is 3.0, yet your
> > input
> > > > > has it going from 3.783 to 3.5. This seems to be a problem, for some
> > > > reason
> > > > > sander is not reading your input file correctly. Can you confirm that
> > > > this
> > > > > is the case?
> > > > >
> > > > > also, is there anything unusual about the solvent? is it just TIP3P
> > > > water?
> > > > > and no solvent molecules or ions are in the tgt masks? are all atoms
> > in
> > > > the
> > > > > masks in the same actual molecule? try to think of anything unusual
> > about
> > > > > your setup.
> > > > >
> > > > > also, have you visualized the output trajectory?
> > > > >
> > > > >
> > > > > On Fri, Mar 30, 2012 at 9:49 AM, Fredrick Devadoss <
> > > > > Fredrick.Devadoss.uni-konstanz.de> wrote:
> > > > >
> > > > > > Dear Carlos and others,
> > > > > >
> > > > > > Here is the sander input:
> > > > > >
> > > > > > targeted molecular dynamics run
> > > > > > &cntrl
> > > > > > imin=0, ntx=5, nstlim=500000, irest=1,
> > > > > > dt=0.002, ntc=2, ntf=2, tol=0.000001,
> > > > > > tempi=100.0, temp0=300.0,
> > > > > > scee=1.2, cut=12.0, iwrap=1,
> > > > > > ntpr=1000, ntwx=1000, ntwr=1000,
> > > > > > ntb=1, ntt=1, tautp=0.5, ntp=0,
> > > > > > igb=0, nscm=0, nmropt=1,
> > > > > > tgtfitmask=":1-158, 351-360, 493-544, 548-554",
> > > > > > itgtmd=1, tgtrmsd=3.783, tgtmdfrc=0.5,
> > > > > > tgtrmsmask=":159-350, 361-492, 545-547, 555-557",
> > > > > > /
> > > > > > &wt
> > > > > > TYPE='TGTRMSD', istep1=1, istep2=500000,
> > > > > > value1=3.783, value2=3.500,
> > > > > > /
> > > > > > &wt
> > > > > > type="END",
> > > > > > /
> > > > > >
> > > > > > Warm regards
> > > > > > Fredrick.
> > > > > >
> > > > > >
> > > > > > On Friday, March 30, 2012 15:41 CEST, Carlos Simmerling <
> > > > > > carlos.simmerling.gmail.com> wrote:
> > > > > >
> > > > > > > can you just paste the sander input to an email as text?
> > > > > > >
> > > > > > >
> > > > > > > On Fri, Mar 30, 2012 at 9:34 AM, Fredrick Devadoss <
> > > > > > > Fredrick.Devadoss.uni-konstanz.de> wrote:
> > > > > > >
> > > > > > > > Dear Carlos and other AMBER users/developers,
> > > > > > > >
> > > > > > > > The simulations were done with AMBER 10 and you can find the
> > input
> > > > > > files
> > > > > > > > in the following link:
> > > > > > > >
> > > > > > > > http://www.tcd.uni-konstanz.de/AMBER_MAIL/amber.tar
> > > > > > > >
> > > > > > > > Expecting your replies and thanks in advance.
> > > > > > > >
> > > > > > > > Warm regards
> > > > > > > > Fredrick.
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > On Friday, March 30, 2012 14:52 CEST, Carlos Simmerling <
> > > > > > > > carlos.simmerling.gmail.com> wrote:
> > > > > > > >
> > > > > > > > > Please include your input file so we can see what you are
> > trying
> > > > to
> > > > > > do.
> > > > > > > > > Also tell us the amber version.
> > > > > > > > > On Mar 30, 2012 8:20 AM, "Fredrick Devadoss" <
> > > > > > > > > Fredrick.Devadoss.uni-konstanz.de> wrote:
> > > > > > > > >
> > > > > > > > > > Dear AMBER users and developers:
> > > > > > > > > >
> > > > > > > > > > We run into a problem with targeted MD and we have
> > absolutely
> > > > no
> > > > > > clue
> > > > > > > > what
> > > > > > > > > > causes them. We first run 10ns of normal MD simulations on
> > the
> > > > > > system
> > > > > > > > > > without any problem. Then we started the targeted MD.
> > After a
> > > > few
> > > > > > > > steps, we
> > > > > > > > > > see a large jump of more than 50000 kcal/mole in the total
> > > > energy
> > > > > > (see
> > > > > > > > > > attached file and summary below). We analyzed this
> > behavior in
> > > > > > detail
> > > > > > > > and
> > > > > > > > > > the change is due to extremely more favorable electrostatic
> > > > > > > > interactions of
> > > > > > > > > > the solvents molecules. But by visual inspection, no large
> > > > > > difference
> > > > > > > > can
> > > > > > > > > > be seen. The simulation box has the same size (another
> > behavior
> > > > > > would
> > > > > > > > have
> > > > > > > > > > been very surprising since we did a NVT simulation but you
> > > > never
> > > > > > know)
> > > > > > > > and
> > > > > > > > > > also the protein does not change much (all-atom rmsd
> > difference
> > > > > > before
> > > > > > > > and
> > > > > > > > > > after the energy jump of 1 .4 Angstrom). Also some other
> > > > > > simulations
> > > > > > > > on the
> > > > > > > > > > same system but with other restraint mask show the same
> > > > behavior
> > > > > > even
> > > > > > > > if
> > > > > > > > > > the energy jumps sometimes start much later in the
> > simulation.
> > > > Does
> > > > > > > > anybody
> > > > > > > > > > has an idea what can be
> > > > > > > > > > going wrong here.
> > > > > > > > > >
> > > > > > > > > > The system is a DNA-protein complex and we are happy to
> > share
> > > > the
> > > > > > > > input as
> > > > > > > > > > well as the output. But due to size limitations, we cannot
> > > > attach
> > > > > > them
> > > > > > > > > > directly to this email. Thus, we would put them on our web
> > > > server
> > > > > > on
> > > > > > > > demand.
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > >
> > > > > >
> > > >
> > ===============================================================================
> > > > > > > > > >
> > > > > > > > > > A V E R A G E S O V E R 500000 S T E P S
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > NSTEP = 500000 TIME(PS) = 12700.000 TEMP(K) =
> > 302.76
> > > > > > PRESS =
> > > > > > > > > > 0.0
> > > > > > > > > > Etot = -243182.8774 EKtot = 43990.9686 EPtot
> > > > =
> > > > > > > > > > -287173.8460
> > > > > > > > > > BOND = 711.6154 ANGLE = 2039.5414 DIHED
> > > > =
> > > > > > > > > > 5355.1836
> > > > > > > > > > 1-4 NB = 1906.4843 1-4 EEL = 11768.4366 VDWAALS
> > > > =
> > > > > > > > > > 38849.0992
> > > > > > > > > > EELEC = -347819.8167 EHBOND = 0.0000
> > RESTRAINT
> > > > =
> > > > > > > > > > 15.6103
> > > > > > > > > > EAMBER (non-restraint) = -287189.4563
> > > > > > > > > > Ewald error estimate: 0.7088E-04
> > > > > > > > > > Current RMSD from reference: 3.193
> > > > > > > > > > Current target RMSD: 3.000
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > >
> > > > > >
> > > >
> > ------------------------------------------------------------------------------
> > > > > > > > > >
> > > > > > > > > > NMR restraints: Bond = 0.000 Angle = 0.000
> > Torsion
> > > > =
> > > > > > > > 0.000
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > >
> > > > > >
> > > >
> > ===============================================================================
> > > > > > > > > >
> > > > > > > > > > R M S F L U C T U A T I O N S
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > NSTEP = 500000 TIME(PS) = 12700.000 TEMP(K) =
> > 1.73
> > > > > > PRESS =
> > > > > > > > > > 0.0
> > > > > > > > > > Etot = 14406.0444 EKtot = 252.0661 EPtot
> > > > =
> > > > > > > > > > 14630.3082
> > > > > > > > > > BOND = 369.4600 ANGLE = 885.9235 DIHED
> > > > =
> > > > > > > > > > 234.8907
> > > > > > > > > > 1-4 NB = 75.4107 1-4 EEL = 32.6070 VDWAALS
> > > > =
> > > > > > > > > > 2705.6396
> > > > > > > > > > EELEC = 15698.4882 EHBOND = 0.0000
> > RESTRAINT
> > > > =
> > > > > > > > > > 14.8110
> > > > > > > > > > EAMBER (non-restraint) = 14615.4972
> > > > > > > > > > Ewald error estimate: 0.3253E-04
> > > > > > > > > > Current RMSD from reference: 3.193
> > > > > > > > > > Current target RMSD: 3.000
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > >
> > > > > >
> > > >
> > ------------------------------------------------------------------------------
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > Your replies are highly appreciated.
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > Warm regards
> > > > > > > > > > Fredrick Robin Devadoss V.
> > > > > > > > > > Ph.D. Student
> > > > > > > > > > Dr. Thomas Exner Group
> > > > > > > > > > University of Konstanz
> > > > > > > > > > Konstanz, Germany.
> > > > > > > > > >
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Received on Wed Apr 04 2012 - 06:00:05 PDT
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