How about use the latest AmberTools for this? I think you two are using
different versions.
Qin, could you confirm that you are using the latest AmberTools?
All the best,
Ray
On Wed, May 16, 2012 at 8:09 PM, Sudarshan Debnath <
sudarshandebnath.ku.rediffmail.com> wrote:
> 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 Thu May 17 2012 - 10:00:02 PDT
