thanks mate!
Igor Marques
On Thu, May 26, 2011 at 6:12 PM, Justin A. Lemkul <[email protected]> wrote:
>
>
> Igor Marques wrote:
>
>> dear all,
>>
>> regarding the matter of electron density, can anyone clarify me on the
>> output units?
>> from this discussion i understand the values are presented in
>> electrons/A^3 - is this correct?
>>
>>
> No. It is electrons/nm^3. Standard units are defined in Chapter 2 of the
> manual (and printed in the code, of course).
>
> -Justin
>
> best regards,
>> igor
>>
>>
>> Igor Marques
>>
>> Molecular Modeling Group – Univ. of Aveiro
>> http://molecular-modeling.dq.ua.pt/
>>
>>
>>
>> On Sat, Jan 1, 2011 at 9:01 PM, Jianhui Tian <[email protected]<mailto:
>> [email protected]>> wrote:
>>
>> Problem solved.
>> The "2" in the text is just a typo when I sent the email.
>> So actually there is no partial charge in the electrons.dat file.
>> Thanks, Justin.
>>
>> Jianhui
>>
>> Date: Sat, 01 Jan 2011 13:56:45 -0500
>>
>> From: "Justin A. Lemkul" <[email protected] <mailto:[email protected]>>
>> Subject: Re: [gmx-users] electron density
>> To: Discussion list for GROMACS users <[email protected]
>> <mailto:[email protected]>>
>> Message-ID: <[email protected] <mailto:[email protected]>>
>>
>>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>>
>>
>> Jianhui Tian wrote:
>> > Date: Fri, 31 Dec 2010 19:08:50 -0500
>> > From: "Justin A. Lemkul" <[email protected]
>> <mailto:[email protected]> <mailto:[email protected]
>>
>> <mailto:[email protected]>>>
>> > Subject: Re: [gmx-users] electron density
>> > To: Discussion list for GROMACS users <[email protected]
>> <mailto:[email protected]>
>> > <mailto:[email protected] <mailto:[email protected]>>
>>
>> >
>> > Message-ID: <[email protected]
>> <mailto:[email protected]> <mailto:[email protected]
>>
>> <mailto:[email protected]>>>
>> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> >
>> >
>> >
>> > Jianhui Tian wrote:
>> >> Hi gmx users,
>> >>
>> >> I tried to calculate both the mass density and electron density
>> for the
>> >> water layer of a membrane simulation. The mass density is 1000
>> kg/m^3,
>> >> however the electron density I got is smaller than about 0.33
>> e/A^3. I
>> >
>> >> How much smaller?
>> > I got about 0.27 e/A^3.
>> >
>> >> am using a CHARMM force field and the CHARMM version of TIP3P
>> water. Am
>> >> I doing anything wrong when calculating the electron density?
>> Thanks a
>> > lot.
>> >>
>> >
>> >> Possibly, but without seeing what you used for input, information
>> > about your
>> >> simulation, etc it's impossible to say.
>> > In the electrons.dat file, I had
>> > 2
>> > OW = 8.834
>> > HW1 = 0.583
>> > HW2 = 0.583
>> > And then used g_density ... -ei electrons.dat -dens electron ...
>> >
>>
>> There are several problems. The first line of electrons.dat
>> indicates there are
>> only two unique atom names, but clearly you're supplying three.
>> Second, this
>> file is read in such that at integral number of electrons is
>> detected on each
>> line. So, in your case, two lines are being read, one that detects
>> 8 electrons,
>> and another that detects zero.
>>
>> -Justin
>>
>> --
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>>
> --
> ========================================
>
> 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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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