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From: <xhu1.memphis.edu>

Date: Tue, 28 Sep 2004 10:19:32 -0600

Dear amber users,

I try to use delphi and UHBD to do MM-PBSA. 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 10E-6 (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 #.#) :0.1000E-05

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 :0.2445E-02

Convergence achieved :0.9680E-06

ITERATION SUMMARY

Iterations required : 189

Norm of the constant vector :0.2526E+04

Norm of the residual vector :0.2445E-02

Convergence achieved :0.9680E-06

######################################################################

In delphi, I choose statement "RMSC" with the same value and

convergence can not be achieved at the required value in 1200 steps:

######################################################################

rms-change 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

.............. ........ .. .. ..........

6.6439105E-05 2.4414063E-04 at 1120 iterations

6.6107619E-05 2.4414063E-04 at 1130 iterations

6.5878099E-05 2.4414063E-04 at 1140 iterations

6.5984161E-05 2.4414063E-04 at 1150 iterations

6.5964879E-05 2.4414063E-04 at 1160 iterations

6.5717104E-05 2.4414063E-04 at 1170 iterations

6.6142711E-05 2.4414063E-04 at 1180 iterations

6.6114844E-05 2.4414063E-04 at 1190 iterations

6.5725071E-05 2.4414063E-04 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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Received on Tue Sep 28 2004 - 17:53:00 PDT

Date: Tue, 28 Sep 2004 10:19:32 -0600

Dear amber users,

I try to use delphi and UHBD to do MM-PBSA. 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 10E-6 (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 #.#) :0.1000E-05

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 :0.2445E-02

Convergence achieved :0.9680E-06

ITERATION SUMMARY

Iterations required : 189

Norm of the constant vector :0.2526E+04

Norm of the residual vector :0.2445E-02

Convergence achieved :0.9680E-06

######################################################################

In delphi, I choose statement "RMSC" with the same value and

convergence can not be achieved at the required value in 1200 steps:

######################################################################

rms-change 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

.............. ........ .. .. ..........

6.6439105E-05 2.4414063E-04 at 1120 iterations

6.6107619E-05 2.4414063E-04 at 1130 iterations

6.5878099E-05 2.4414063E-04 at 1140 iterations

6.5984161E-05 2.4414063E-04 at 1150 iterations

6.5964879E-05 2.4414063E-04 at 1160 iterations

6.5717104E-05 2.4414063E-04 at 1170 iterations

6.6142711E-05 2.4414063E-04 at 1180 iterations

6.6114844E-05 2.4414063E-04 at 1190 iterations

6.5725071E-05 2.4414063E-04 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

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

The AMBER Mail Reflector

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To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Tue Sep 28 2004 - 17:53:00 PDT

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