AMBER Archive (2009)

Subject: [AMBER] Umbrella test

From: Arnaud (arnaud_at_lcc-toulouse.fr)
Date: Thu Apr 02 2009 - 04:51:01 CDT

Hello,

I runed umbrella sampling with amber8 and amber10 with the parameters file
given in amber manual :

************************************
test of umbrella sampling of a chi torsion angle
 &cntrl
   nstlim=50000, cut=20.0, igb=1, saltcon=0.1,
   ntpr=1, ntwr=100000, ntt=3, gamma_ln=0.2,
   ntx=5, irest=1,
   ntc=2, ntf=2, tol=0.000001,
   dt=0.001, ntb=0,
   nmropt=1,
 /
 &wt type='DUMPFREQ', istep1=10 /
 &wt type='END' /
DISANG=chi.RST
DUMPAVE=chi_vs_t.170
EOF
**************************************

chi.RST, prmtop and md4.x files needed for this calculation were those
proposed in test directory of amber package.

Begin and end results in chi_vs_t.170 file obtained with amber10 were :
       0 28.408
      10 76.692
      20 103.804
      30 106.999
      40 101.039
      50 93.077
      60 109.138
      70 119.145
      80 142.406
      90 133.365
     100 128.226
     110 117.133
...
   49900 169.076
   49910 171.938
   49920 170.164
   49930 170.135
   49940 170.565
   49950 171.870
   49960 173.956
   49970 172.371
   49980 172.124
   49990 170.298
 

Begin and end results in chi_vs_t.170 obtained with amber8 were :
       0 28.408
      10 76.756
      20 103.865
      30 107.183
      40 101.340
      50 94.314
      60 109.482
      70 119.648
      80 141.769
      90 132.950
     100 128.029
     110 118.266
...
   49900 166.738
   49910 162.640
   49920 166.876
   49930 172.380
   49940 173.665
   49950 167.582
   49960 163.551
   49970 166.160
   49980 166.259
   49990 164.893

*******************************

Why these differences of results ?

P.S :I also runed this test for amber9 and in this case results were
identical to those obtained with amber10

Best regards,

Philippe

___________________________________________________________________
CNRS / Laboratoire de Chimie de Coordination

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