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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Received on Sun Nov 12 2006 - 06:07:10 PST
