Dear Carlos,
As you suggested in one of your earlier mails, we have revisited the NSCM, assigned it to the default value, and ran the TMD simulation again. Now, there are no energy jumps as well as flying ice-cube effect.
We would like to thank you for your efforts (looking into the system, inputs and outputs), for the discussions and suggestions.
Thanks & Regards
Fredrick.
On Thursday, April 12, 2012 14:22 CEST, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
> what I see in these outputs reinforces my suspicion that it isn't the tgtmd
> that is the main issue here. for example, in md3.out the bond energy drops
> significantly during the run. To me, that's a sign of poor partitioning of
> energy among different motions. When I see this I suspect the "flying ice
> cube". Take a look at my previous email and start to troubleshoot from
> there. For example, have you visualized the trajectory?
>
> On Wed, Apr 4, 2012 at 8:34 AM, Fredrick Devadoss <
> Fredrick.Devadoss.uni-konstanz.de> wrote:
>
> > Dear Carlos,
> >
> > Thank you very much for your reply. Herewith I have enclosed the two mdout
> > files for your perusal.
> >
> > md1.out - 1ns output file of the TMD simulation.
> > md3.out - 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 Tue Apr 17 2012 - 03:00:03 PDT
