Hi
In addition to my just sent reply I have pasted here box system info
outputs both from AMBER and GROMACS and one can see significant Volume
difference (NOTE: Gromacs measures in nm)
_____________________________________________________________
command: solvateoct hex20 TIP3PBOX 12.0
###### AMBER output
Scaling up box by a factor of 1.271723 to meet diagonal cut criterion
Solute vdw bounding box: 73.650 148.477 85.403
Total bounding box for atom centers: 178.998 178.998 178.998
(box expansion for 'iso' is 165.3%)
Solvent unit box: 18.774 18.774 18.774
Volume: 2915924.151 A^3 (oct)
Total mass 1637719.276 amu, Density 0.933 g/cc
Added 82336 residues.
Checking Unit.
------------------------------------------------------------------------------------------------------
_______________________________________________________________
command: editconf -f input.gro -o output.gro -c -d 1.2 -bt octahedron
#####GROMACS output
system size : 12.324 14.348 5.952 (nm)
diameter : 15.385 (nm)
center : 7.774 7.569 7.829 (nm)
box vectors : 12.324 14.348 5.952 (nm)
box angles : 90.00 90.00 90.00 (degrees)
box volume :1052.41 (nm^3)
shift : 1.119 5.007 -0.568 (nm)
new center : 8.893 12.576 7.261 (nm)
new box vectors : 17.785 17.785 17.785 (nm)
new box angles : 70.53 109.47 70.53 (degrees)
new box volume :4330.63 (nm^3)
-------------------------------------------------------------------------------------------------------------
On Sun, Jun 15, 2014 at 3:18 PM, newamber list <newamberlist.gmail.com>
wrote:
> Hi Murat and Jason
>
> Thanks for your replies
>
> That was nice suggestion Murat and I should try that as I am also not able
> to find the reason for this great number of difference in water molecules.
>
> and Also ...
>
> >> However, you can always experiment with Amber and keep making the
> buffer size a little larger until you get _almost_ the number of water
> molecules you want, plus a small number more.
>
> But the problem now is which one to believe Gromacs' or Amber's number of
> water :( I ran initial job with AMBER and want to compare with Gromacs and
> now found such a great difference with Gromacs. Changing the buffer size to
> get same water molecules would be a problem in reporting in future. Say
> with AMBER I used 12 Angs buffer and with Gromacs I used 8 Angs buffer to
> keep waters same. That does not sound correct to report in publications :(
>
> >> Since I don't know any specifics about gromacs, I don't know how to specifically
> help
>
> I had put same query in Gromacs archive and they also dont know what AMBER
> does but I am posting here what Tsjerk Wassenaar from Gromacs replied.
> Hope it helps to find the reason.
>
> Gromacs query title:"" truncated octahedron box vector angles and number
> of waters""
>
> ""
> .... As for the difference
> in water molecules, I don't know what AMBER does, but I can tell what
> Gromacs does. You have the diameter of the system, 15.385 nm, to which
> <<<# diameter is basically the longest length #>>>
> twice the 1.2 nm is added, giving the vector length 17.785 nm. A cube of
> that length would have a volume of 5625 nm^3, and a truncated octahedron is
> about 78% the volume of a cube, so it gives 0.78*(17.785**3) = 4388 nm^3.
> Well, there's some rounding..., the 4330.63 will be correct. Solvating that
> with genbox should give a pretty much correct amount of water. If AMBER
> gives you so much less, I'd guess there's something odd there.""
>
>
> Thanks
>
>
>
> On Sun, Jun 15, 2014 at 6:07 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
>> On Fri, Jun 13, 2014 at 9:04 AM, newamber list <newamberlist.gmail.com>
>> wrote:
>>
>> > Hi All
>> >
>> > I am solvating same system with truncated octahedron box and want to run
>> > with both AMBER and GROMACs. In AMBER, am using 12 Ang buffer with
>> > solvateoct and get around 76716 water molecules but with Gromacs with
>> same
>> > buffer I am getting around 132902 waters (almost twice). These are
>> > following commands am using:
>> >
>> >
>> > with AMBER:
>> > solvateoct sol TIP3PBOX 12
>> >
>> > with GROMACS:
>> > editconf -f input.gro -o output.gro -c -d 1.2 -bt octahedron
>> >
>> >
>> > I am not sure whats wrong, please let me know if someone got similar
>> > issues?
>> >
>>
>> I'm not familiar with Gromacs at all. However, you can always experiment
>> with Amber and keep making the buffer size a little larger until you get
>> _almost_ the number of water molecules you want, plus a small number more.
>>
>> Then you can use ParmEd or cpptraj to create a new topology file by
>> stripping away the "extra" water molecules.
>>
>> In order for GROMACS and Amber to be getting that big of a difference in
>> the total number of solvent molecules, they must be doing different
>> things.
>> Since I don't know any specifics about gromacs, I don't know how to
>> specifically help.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Sun Jun 15 2014 - 08:30:02 PDT
