VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Aug 05 2005 - 17:46:25 CDT

Which is what NAMD reports. Measuring the minmax of the output
coordinates is only useful if you're wrapping, and then it's with an error
due to the size of the molecules that stick out the edges. Right now it
doesn't even look like your system is filling the periodic cell in the x
and y dimensions.

-Jim

On Fri, 5 Aug 2005, Brian Bennion wrote:

>
> yes this is correct, however, I am in the NVE ensemble and therefore my
> system should not change its volume.
>
> Brian
>
> On Fri, 5 Aug 2005, Jim Phillips wrote:
>
>>
>> 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
>>> ************************************************
>>>
>>
>
> ************************************************
> 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
> ************************************************
>