Tutorial-l Mailing List

From: Timothy Isgro (timisgro_at_ks.uiuc.edu)
Date: Sat Mar 17 2007 - 16:37:00 CDT

Hi Won-Young,
I think the simplest way to measure density is to count the number of
molecules along with the volume they occupy. For water density in a
water box, this may be done using something like:

set sel [atomselect top water]
puts [expr [ $sel num]/3 ]
    #get number of water molecules (divide by 3 since [$sel num]
gives the number of water *atoms*)
measure minmax $sel
    #get the extent of the water box (from which to calculate volume)

Keep in mind that determining volumes by which to measure density in
all-atom systems (especially as they get smaller) can be a "grey"
area, since you're dealing with individual atoms and not "bulk"
solvent. Also, for shapes which are not as simple as a water box,
you may need to do something more clever, like split the region into
different shapes (e.g. spheres) whose volume can be measured.

In addition, we also have a stand-alone program to estimate molecular
volumes. Perhaps this can be of some use.
http://www.ks.uiuc.edu/Development/MDTools/molvolume/

-Tim

On Mar 16, 2007, at 3:22 PM, <wahn_at_uiuc.edu> <wahn_at_uiuc.edu> wrote:

> Thank you for the information.
> Is there any way to measure the system density in VMD?
>
> Won-Young
>
> ---- Original message ----
>> Date: Fri, 16 Mar 2007 12:55:34 -0500
>> From: Timothy Isgro <timisgro_at_ks.uiuc.edu>
>> Subject: Re: tutorial-l: Water density in a periodic box
>> To: "<wahn_at_uiuc.edu>" <wahn_at_uiuc.edu>
>> Cc: tutorial-l_at_ks.uiuc.edu
>>
>> Hi Won-Young,
>> By typing "solvate" in the TkCon (Extensions > Tk Console), you will
>> see all the options which you can specify for the solvate package.
>> Of particular interest to you might be the -b option which defines
>> the minimum distance between water and solute molecule(s). Default
>> is 2.4 A, so reducing this number may allow for waters to be placed
>> in the small "hollow spaces" you talk about. If that doesn't work,
>> you may also try to place water molecules by hand (perhaps by moving
>> some bulk solvent waters using VMD's move command). You may also be
>> interested in the DOWSER program, which surveys molecules the asses
>> the hydrophobic/hydrophilic nature of their cavities, etc.
>> http://hekto.med.unc.edu:8080/HERMANS/software/DOWSER/
>> -Tim
>>
>> On Mar 14, 2007, at 2:46 PM, <wahn_at_uiuc.edu> <wahn_at_uiuc.edu> wrote:
>>
>>> Dear NAMD users,
>>>
>>> How do you solvate your protein or whatever the molecule?
>>>
>>> I have used the solvation function of VMD.
>>> But, my system after solvation does not have enough water molecules
>>> and contains a kind of hollow space in it.
>>>
>>> How may I adjust and measure the water density of my system?
>>>
>>> Your comment could save me a lot of time and efforts.
>>> Thank you.
>>>
>>> Won-Young
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>>
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