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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> > > > >
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> > >
> > >
> > >
> > >
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Received on Tue Apr 03 2012 - 08:30:04 PDT
