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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Received on Sun Jul 13 2008 - 06:07:34 PDT
