Justin A. Lemkul
jalemkul at vt.edu
Thu Mar 11 21:26:04 CET 2010
nishap.patel at utoronto.ca wrote:
> Hi Justin,
> Well from the previous post:
> The number density for water should be about 32.5 waters per cubic
> nanometer. So if my box size is 4 4 4 =64nm^3, then shouldn't number of
> water molecules be 64*32.5 = 2080? May be I am not understanding it
> correctly. I am using Tip3p water model for my simulations.
Using which .gro file for genbox? One that is specifically for TIP3P (i.e.,
from the ffamber ports), or just spc216.gro? Keep in mind, as well, that
simulation water is not the same as real water, so densities and other
properties are going to be dependent upon the water model. Based on the
calculation I just presented, that works out to be almost exactly the number you
ended up with. From ffamber_tip3p.gro, you'd get about 2130 waters for that
given box size.
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>> nishap.patel at utoronto.ca wrote:
>>> I am trying to use genbox to add water molecules to my system
>>> consisting of one molecule of ethane in the box size of 4 4 4nm(
>>> 64nm^3). If I understand it correctly, with the system of that size,
>>> I should have ~2080 water molecules in my system, but instead genbox
>>> adds ~2177 molecules of water, with higher density (1018.63 (g/l)).
>>> Is that correct?
>> Should be, but you haven't said what model water you're using.
>> Assuming SPC, the box you've specified is 10x the size of spc216.gro,
>> so I would expect that genbox would add roughly 216 x 10 = 2160
>> molecules, give or take a few. How did you come up with 2080 as the
>> expected value?
>>> Nisha Patel
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
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> Nisha Patel
> MSc Candidate
> Leslie Dan Faculty of Pharmacy
> Department of Pharmaceutical Sciences
> 144 College Street
> Room 1172
> Toronto, ON
> M5S 3M2
> Telephone: 416-978-1536
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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