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.
> > > > > >
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Received on Fri Mar 30 2012 - 11:30:04 PDT
