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
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
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Received on Fri Mar 30 2012 - 07:00:04 PDT
