Dear Ray,
I analyzed the two mdout file (Qin and mine) more rigorously and find the following difference. I think that the calculations of pbsa for electrostatic potential are not same for Qin and me. But I can not find out why it is different? The following difference may be helpful to find the problem for You and Others.
The difference between two mdout file as follows-
1st difference:
Qin mdout
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
Potential function:
ntf = 1, ntb = 1, ipb = 1, nsnb = 25
My mdout
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
Potential function:
ntf = 1, ntb = 1, igb = 10, nsnb = 25
2nd difference:
Qin mdout
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
NB-update: atom-based nb list 9199
My mdout
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
NB-update: residue-based nb list 14972
NB-update: atom-based nb list 9199
3rd difference:
Qin mdout
======== Setting up Grid Parameters ========
Using bounding box for grid setup
Bounding Box at level: 2
Bounding Box Center: 7.000 65.000 114.000
Xmin, Xmax, Xmax-Xmin: -3.759 17.794 21.553
Ymin, Ymax, Ymax-Ymin: 55.004 74.249 19.245
Zmin, Zmax, Zmax-Zmin: 106.134 120.944 14.810
beginning box center at level 2 7.000 65.000 114.000
Grid dimension at level 2 41 41 41
Grid origin corrected at level 2 -14.000 44.000 93.000
Bounding Box at level: 1
Bounding Box Center: 7.000 65.000 114.000
Xmin, Xmax, Xmax-Xmin: -3.759 17.794 21.553
Ymin, Ymax, Ymax-Ymin: 55.004 74.249 19.245
Zmin, Zmax, Zmax-Zmin: 106.134 120.944 14.810
beginning box center at level 1 7.000 65.000 114.000
Grid dimension at level 1 7 7 7
Grid origin corrected at level 1 -25.000 33.000 82.000
------- VMD goodie --------
#First Level Geometric Box
draw materials off
draw color green
draw line " -25.000 33.000 82.000" " 31.000 33.000 82.000"
draw line " -25.000 33.000 82.000" " -25.000 89.000 82.000"
draw line " -25.000 33.000 82.000" " -25.000 33.000 138.000"
draw line " 31.000 33.000 82.000" " 31.000 89.000 82.000"
draw line " 31.000 33.000 82.000" " 31.000 33.000 138.000"
draw line " -25.000 89.000 82.000" " 31.000 89.000 82.000"
draw line " -25.000 89.000 82.000" " -25.000 89.000 138.000"
draw line " -25.000 33.000 138.000" " 31.000 33.000 138.000"
draw line " -25.000 33.000 138.000" " -25.000 89.000 138.000"
draw line " 31.000 89.000 138.000" " 31.000 89.000 82.000"
draw line " 31.000 89.000 138.000" " -25.000 89.000 138.000"
draw line " 31.000 89.000 138.000" " 31.000 33.000 138.000"
#2nd Level Geometric Box
draw color blue
draw line " -14.000 44.000 93.000" " 28.000 44.000 93.000"
draw line " -14.000 44.000 93.000" " -14.000 86.000 93.000"
draw line " -14.000 44.000 93.000" " -14.000 44.000 135.000"
draw line " 28.000 44.000 93.000" " 28.000 86.000 93.000"
draw line " 28.000 44.000 93.000" " 28.000 44.000 135.000"
draw line " -14.000 86.000 93.000" " 28.000 86.000 93.000"
draw line " -14.000 86.000 93.000" " -14.000 86.000 135.000"
draw line " -14.000 44.000 135.000" " 28.000 44.000 135.000"
draw line " -14.000 44.000 135.000" " -14.000 86.000 135.000"
draw line " 28.000 86.000 135.000" " 28.000 86.000 93.000"
draw line " 28.000 86.000 135.000" " -14.000 86.000 135.000"
draw line " 28.000 86.000 135.000" " 28.000 44.000 135.000"
--- End VMD goodie --------
My mdout
======== Setting up Grid Parameters ========
Using bounding box for grid setup
Bounding Box Center: 7.000 65.000 114.000
Xmin, Xmax, Xmax-Xmin: -3.759 17.794 21.553
Ymin, Ymax, Ymax-Ymin: 55.004 74.249 19.245
Zmin, Zmax, Zmax-Zmin: 106.134 120.944 14.810
beginning box center at level 1 7.000 65.000 114.000
beginning box center at level 2 7.000 65.000 114.000
Grid dimension at level 1 7 7 7
Grid origin corrected at level 1 -25.000 33.000 82.000
Grid dimension at level 2 41 41 41
Grid origin corrected at level 2 -14.000 44.000 93.000
4th difference:
Qin mdout
======== Setting up Solvent Accessibility Data ========
Setting up working radii
Number of SA srf points exposed 5780
Number of SA arcs generated 3731
Number of SA arc points exposed 13214 with resolution (A) = .625000E-01
My mdout
======== Setting up Solvent Accessibility Data ========
Setting up working radii
Found nonzero radii 179
Number of SA srf points exposed 5780
Number of SA arcs generated 3731
Number of SA arc points exposed 13218 with resolution (A) 0.0625
5th difference:
Qin mdout
Boundary conditions
sum of grid charges as independent DH spheres
My mdout
Boundary conditions
electrostatic focus boundary condition
6th difference:
Qin mdout
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Total time 0.45
| Read prm/crd time 0.07
| Force time 0.38
| Nonbond force 0.38
| PB Nonbond 0.38
| PB NB list 0.00
| PB FD grid 0.02
| PB Sasa 0.14
| PB FD force 0.21
| PB Set linear sys 0.06
| PB Solver 0.12
| PB SA arc 0.13
| PB SA arc setup 0.00
| PB circle 0.07
| PB exclude 0.06
| PB exmol 0.06
| PB exmol setup 0.00
| PB exmol part a 0.00
| PB exmol part b 0.01
| PB exmol part e 0.00
| PB exmol part f 0.04
| PB epsbnd 0.00
| PB epsmap 0.00
| Job began at 11:21:57.652 on 04/30/2012
| Setup done at 11:21:57.723 on 04/30/2012
| Run done at 11:21:58.098 on 04/30/2012
| wallclock() was called 84 times
My mdout:
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Total time 0.78
| Read prm/crd time 0.03
| Force time 0.76
| Nonbond force 0.76
| PB Nonbond 0.76
| PB NB list 0.00
| PB FD grid 0.41
| PB FD Force 0.35
| PB Epsmap 0.13
| PB Solver 0.20
| Job began at 06:29:34.573 on 01/01/2004
| Setup done at 06:29:34.599 on 01/01/2004
| Run done at 06:29:35.358 on 01/01/2004
| wallclock() was called 34 times
With best regards,
Sudarshan.
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Received on Wed May 16 2012 - 20:30:03 PDT
