VMD-L Mailing List

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Aug 05 2005 - 16:12:34 CDT

Hello,

I have been doing some checking and am a bit puzzled by significant
differences in volume/minmax values for my system as I prep it.

Shown below is a list of the dimensions from VMD, while my NAMD logs show
a constant value of 923636.6390. As you can see there is a significant
difference between ^^^^^^^^^^^ and 964243.

Any ideas?

Brian

The first protein structure after solvation
vmd > measure center atomselect0
56.7788696289 53.1865577698 28.926109314
vmd > measure minmax atomselect0
{9.60099983215 7.13899993896 -9.27499961853} {103.963996887 99.2289962769
67.18699646}
113.56499671915,106.36799621586,76.46199607853

The first protein minimization
vmd > measure center atomselect1
56.7812080383 53.1876869202 28.9241199493
vmd > measure minmax atomselect1
{9.60099983215 7.13899993896 -9.27499961853} {103.963996887 99.2289962769
67.18699646}
113.56499671915,106.36799621586,76.46199607853 = 923636.53205419

The first water minimization
vmd > measure center atomselect2
56.7821578979 53.1882400513 28.9262428284
vmd > measure minmax atomselect2
{7.91300010681 5.50600004196 -10.3170003891} {105.897003174 101.152999878
68.3010025024}
113.81000328081,106.65899991996,78.6180028915 = 954333.01948221

Combined system minimization
vmd > measure center atomselect3
56.7821617126 53.1882591248 28.9262313843
measure minmax atomselect3
{7.38999986649 5.38500022888 -10.7279996872} {106.850997925 101.248001099
68.4260025024}
114.24099779149,106.63300132788,79.1540021896 = 964243.01025232

System after first heating to 298K
vmd > measure center atomselect4
56.7866363525 53.2055130005 28.868429184
vmd > measure minmax atomselect4
{3.93581748009 0.995232284069 -10.0360746384} {110.403068542 104.675170898
67.9366989136}
114.33888602209,105.67040318207,77.972773552 = 942085.46608153

************************************************
  Brian Bennion, Ph.D.
  Bioscience Directorate
  Lawrence Livermore National Laboratory
  P.O. Box 808, L-448 bennion1_at_llnl.gov
  7000 East Avenue phone: (925) 422-5722
  Livermore, CA 94550 fax: (925) 424-6605
************************************************