[gmx-users] g_sas problem

[tangxuan]

Yes, the default value of -pbc is 'yes'. I did not add it in my command,
but i think pbc should has been considered.  It seems there is no
contact between the two subunits, but at some specific time the total
ASA of interaction region is very high(shown below).

  time     total SAS of interaction region 
  15936   1.16099999999997
  15937   1.09100000000004
  15938   86.954
  15939   1.16899999999998
  15940   1.096
  15941   1.22199999999998
  15942   1.36900000000003
  15943   89.423
  15944   1.328
  15945   91.182
  15946   88.058
  15947   1.33000000000001
  15948   1.154
  15949   1.21799999999996
  15950   89.782
  15951   89.541
  15952   89.549
  15953   89.691
  15954   89.975
  15955   89.018
  15956   88.774
  15957   88.46
  15958   88.859
  15959   89.69
  15960   1.18900000000002
  15961   88.087
  15962   89.248
  15963   89.78
  15964   88.64
  15965   90.222
  15966   1.262
  15967   1.23500000000001
  15968   1.3290000000000

Thanks for your help.

Tang jiaowei
On Tue, 2007-10-30 at 14:57 +0100, David van der Spoel wrote:
> tangxuan wrote:
> > Dear,all
> > When I calculate the accessible surface area(ASA) of interaction region
> > between two subunits A and B in my protein. First I calculated the ASA
> > of A and B by "g_sas -f .xtc -s .tpr -n index.ndx -o .xvg -n index.ndx"
> > respectively. After that, I combined A and B as the one group, then I
> > computed SAS of group A+B in the same way above. When I calculated the
> > hydrophobic SAS of interaction region between A and B by formula
> > (SAS=SAS(A)+SAS(B)-SAS(A+B)), at some specific time this result is
> > negative(the third ps in the result below). But in my opinion, this area
> > should be positive. What is wrong? I can show you the result of the
> > first 3 ps.
> > A:
> >          0     136.923     81.5686     218.491           0
> >          1     136.149     87.5994     223.748           0
> >          2     136.607     90.9957     227.603           0
> > B:      
> >          0     129.967     85.1524     215.119           0
> >          1     140.375      86.953     227.328           0
> >          2     138.37     90.9806      229.35           0
> > A+B:      
> >          0     264.215     169.394     433.608           0
> >          1     274.129     176.945     451.074           0
> >          2     276.924     180.027     456.951           0
> > 
> > Look forward to your explanation.
> 
> Hi Tang,
> 
> I think this is actually a roundoff problem. It looks like your proteins 
> make no contact at all. Did you use the -pbc flag (it may be default though)
> 
> > 
> > Thank you,
> > 
> > Tang Jiaowei
> > 
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