Dear Jason,
The simulation were carried out with AMBER 10. Do the latest version handle this problem? (any idea).
Thanks & Regards
Fredrick.
On Friday, March 30, 2012 21:25 CEST, Jason Swails <jason.swails.gmail.com> wrote:
> Possibly related -- I'm assuming this is Amber 9 or Amber 10, correct?
> I don't know anything about the innards of the TGTMD code, but I think
> it's probably important to know what version of Amber is being used if
> this is a bug...
>
> All the best,
> Jason
>
> On Fri, 2012-03-30 at 20:06 +0200, Fredrick Devadoss wrote:
> > Dear Carlos,
> >
> > Herewith I have enclosed the RMSD and restraint energy plots as attachments.
> >
> > Thanks & Regards
> > Fredrick.
> >
> >
> > On Friday, March 30, 2012 17:57 CEST, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
> >
> > > thanks- also, what does sander say at the start about the current RMSD
> > > value (before MD)? and what is the step 0 or step 1 restraint energy?
> > >
> > >
> > >
> > > 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.
> > > > > > > >
> > > > > > > > _______________________________________________
> > > > > > > > AMBER mailing list
> > > > > > > > AMBER.ambermd.org
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> > > > > > > >
> > > > > > > >
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> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > _______________________________________________
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>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
>
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Received on Fri Mar 30 2012 - 15:30:03 PDT
