[AMBER] Large Energy Jump in TMD simulation - Regarding

From: Fredrick Devadoss <Fredrick.Devadoss.uni-konstanz.de>
Date: Fri, 30 Mar 2012 14:19:56 +0200

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 - 05:30:05 PDT
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