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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Received on Fri Mar 30 2012 - 06:00:06 PDT
