AMBER Archive (2008)

Subject: AMBER: difference between sander and NAB

From: Hu, Shaowen (JSC-SK)[USRA] (Shaowen.Hu-1_at_nasa.gov)
Date: Thu Jul 10 2008 - 14:44:41 CDT

Dear AMBER developers,

Some time ago I reported a difference of MD simulation with GBSA between
sander and NAB, which I did not take serious since I was busy on other
staffs. Now this issue bother me since I am using NAB a lot. I think the
non-polar part of the energy by NAB may have a problem.

Following is the result of single point calculation of sander:

&cntrl
  ntb=0,
 igb=1, saltcon=0.1, gbsa=1,
  cut = 99.0, rgbmax=99.0,
   imin = 1, maxcyc = 1, ncyc = 0,
 &end

NSTEP ENERGY RMS GMAX NAME NUMBER
      1 -5.2401E+03 1.3663E+02 5.8580E+03 H71 2156

 BOND = 89.9247 ANGLE = 636.8464 DIHED =
1462.3030
 VDWAALS = 1500.6878 EEL = -7185.2546 EGB =
-4003.9083
 1-4 VDW = 717.5896 1-4 EEL = 1501.5800 RESTRAINT =
0.0000
 ESURF = 40.1094

and NAB:

  mm_options: ntpr=1
        mm_options: gb=1
        mm_options: gbsa=1
        mm_options: kappa=0.10395
        mm_options: rgbmax=99.
        mm_options: cut=99.0
        mm_options: diel=C
      iter Total bad vdW elect nonpolar genBorn
frms
ff: 0 -4331.38 2189.20 2221.12 -5683.69 945.92 -4003.92
1.37e+02

All terms are close to each other except the nonpolar and Esurf (which I
assume to be the same). The manuals say both of them use the default
LCPO method. Please check why the difference is so large.

Thanks a lot,
Shaowen
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