VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Aug 05 2005 - 17:34:45 CDT

First, you seem to be calculating the volume from minmax as
  volume = (maxx + minx) * (maxy + miny) * (maxz - minz)

If you do it correctly, your system is increasing in volume, with a max of
around 860000 after equilibration. NAMD gives the volume of the periodic
cell, as specified in the config file cellBasisVector[123] or .xsc file.
If the periodic cell is full, then hydrogens will be sticking out the
ends, and minmax will measure a greater volume than the periodic cell.

-Jim

On Fri, 5 Aug 2005, Brian Bennion wrote:

>
>
> 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
> ************************************************
>