AMBER Archive (2004)Subject: AMBER: question about delphi and UHBD
From: xhu1_at_memphis.edu
Date: Tue Sep 28 2004  11:19:32 CDT
Dear amber users,
I try to use delphi and UHBD to do MMPBSA. For the same system, I get
the same coulombic energy, but reaction field energies are totally
different. Input parameters(grid size/dimension, focusing,
internal/solvent dielectric, temperature) are same except convergence
threshold. In UHBD, this value is 1 X 10E6 (it is default value. I
don't know how to change it), and convergence is achieved at 200 steps
or so:
####################################################################
ITERATION VALUES
Maximum iterations (maxi #) : 400
Convergence criteria (conv #.#) :0.1000E05
Linear equation solver flag (solv #) : 1
 incomplete Cholesky preconditioned conjugate gradient
PERFORMING SETUP AND CALCULATION
ITERATION SUMMARY
Iterations required : 189
Norm of the constant vector :0.2526E+04
Norm of the residual vector :0.2445E02
Convergence achieved :0.9680E06
ITERATION SUMMARY
Iterations required : 189
Norm of the constant vector :0.2526E+04
Norm of the residual vector :0.2445E02
Convergence achieved :0.9680E06
######################################################################
In delphi, I choose statement "RMSC" with the same value and
convergence can not be achieved at the required value in 1200 steps:
######################################################################
rmschange max change #iterations
1.0950725E+09 980.2277 at 10 iterations
3.9263824E+08 273.5977 at 20 iterations
1.4039014E+08 148.4565 at 30 iterations
4.9958216E+07 86.13183 at 40 iterations
.............. ........ .. .. ..........
6.6439105E05 2.4414063E04 at 1120 iterations
6.6107619E05 2.4414063E04 at 1130 iterations
6.5878099E05 2.4414063E04 at 1140 iterations
6.5984161E05 2.4414063E04 at 1150 iterations
6.5964879E05 2.4414063E04 at 1160 iterations
6.5717104E05 2.4414063E04 at 1170 iterations
6.6142711E05 2.4414063E04 at 1180 iterations
6.6114844E05 2.4414063E04 at 1190 iterations
6.5725071E05 2.4414063E04 at 1200 iterations
finished qdiffx linear iterations
######################################################################
The final solvation energies for ligand, receptor and complex are
1466, 1529 and 2730 kcal/mol in UHBD and 1035, 1056, 1224
kcal/mol in delphi.
Does anybody have any suggestion to solve this problem? Thank you so
much!
All the best
Shawn HU
Chemistry Department
University of Memphis

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