Hi, all,
I met a question during my MD simulations.
I build one RNA by nucgen mode in AMBER9.
5'- GCAACAGUUACUGCGACGUUU-3'
3'- UUCGUUGUCAAUGACGCUGCA-5'
then add Na+ and was immersed in a truncated octahedral water box with a 8 Å thick solvation shell using TIP3P model for water.
The input file is:
NUC 1
R
G5 C A A C A G U U A C U G C G
A C G U U U3
NUC 2
R
A5 C G U C G C A G U A A C U G
U U G C U U3
END
$ARNA
The protocol is the same as tutorials of DNA in amber website.
When I run MD (heating) with restraints on the solute, it shows:
“ | TOTAL SIZE OF NONBOND LIST = 11362249
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -165850.2011 EKtot = 0.0000 EPtot = -165850.2011
BOND = 70.6432 ANGLE = 293.1576 DIHED = 878.3573
1-4 NB = 343.3582 1-4 EEL = -4205.1036 VDWAALS = 28137.6817
EELEC = -191368.2955 EHBOND = 0.0000 RESTRAINT = 0.0000
Ewald error estimate: 0.9375E-04
------------------------------------------------------------------------------
NSTEP = 100 TIME(PS) = 0.200 TEMP(K) = 60.82 PRESS = 0.0
Etot = -135954.2222 EKtot = 4311.2706 EPtot = -140265.4928
BOND = 119.6398 ANGLE = 360.4977 DIHED = 899.5433
1-4 NB = 355.0263 1-4 EEL = -4202.5635 VDWAALS = 21383.6306
EELEC = -159222.5396 EHBOND = 0.0000 RESTRAINT = 41.2727
EAMBER (non-restraint) = -140306.7655
Ewald error estimate: 0.4724E-04
------------------------------------------------------------------------------
”
The minimisation stage 2- minimising the entire system results is as follows:
“ FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
2500 -1.5472E+05 5.3890E-01 3.1856E+01 H1 26328
BOND = 11197.6011 ANGLE = 293.1576 DIHED = 878.3573
VDWAALS = 28137.6817 EEL = -191368.2955 HBOND = 0.0000
1-4 VDW = 343.3582 1-4 EEL = -4205.1036 RESTRAINT = 0.0000”
I found a rather high van der Waals (VDWAALS and 1-4 VDW) energy although after minimising the entire system. I try lots of methods to eliminate it, such as increase the number of minimisation steps, change the cutoff. But it still does not work. I search this error from amber mailing list and get some information, but cannot solve my question.
Can u give me one advice and explanation?
Thanks for your help,
Ouyang
School of Pharmacy,
University of Queensland
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Received on Sun May 11 2008 - 06:07:04 PDT
