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 - 03:00:05 PDT
