AMBER Archive (2006)

Subject: AMBER: big bond energy change from minimization and md (heating)

From: Rachel (comeonsos_at_googlemail.com)
Date: Wed Nov 08 2006 - 10:40:12 CST

Dear amber users,

I ran minimization for the water only with restraints on the protein first
and then minimized the whole system before i tried to heat up the system,
and I noticed that the bond energy change from the last step of minimization
decreased dramatically when I started to run the equilibration.

Here is the output of the last step of the minimization:
---------------------------------------------------------------------------------------------------------------

NSTEP ENERGY RMS GMAX NAME NUMBER
   5000 -2.0193E+05 5.2652E-01 7.9133E+01 FE 12110

 BOND = 13557.7748 ANGLE = 2100.0258 DIHED =
6683.4797
 VDWAALS = 24316.5978 EEL = -284589.3077 HBOND =
0.0000
 1-4 VDW = 2495.1800 1-4 EEL = 33508.5993 RESTRAINT =
0.0000
------------------------------------------------------------------------------------------------------------------

and here is the output of the equilibration of the system with restraints on
the solute:

-------------------------------------------------------------------------------------------------------------------

 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 17919959
| TOTAL SIZE OF NONBOND LIST = 17919959

 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
 Etot = -215088.9939 EKtot = 0.0000 EPtot = -
215088.9939
 BOND = 396.4313 ANGLE = 2100.0258 DIHED =
6683.4797
 1-4 NB = 2495.1800 1-4 EEL = 33508.5993 VDWAALS =
24316.5978
 EELEC = -284589.3078 EHBOND = 0.0000 RESTRAINT =
0.0000
 Ewald error estimate: 0.1110E-03
 ------------------------------------------------------------------------------

 vlimit exceeded for step 0 ; vmax = Infinity

     Coordinate resetting (SHAKE) was not accomplished
     within 3000 iterations

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.

 ---------------------------------------------------------------------------------------------------------------------

Can anyone suggest how to solve this problem please?

Thanks in advance!

Rachel

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