[gmx-users] Re: density vs time?

[xianghong qi]

Yes, you are right. I didn't apply pressure coupling and my simulation is
under NVT.
I just want to get the density of water vs time . Thanks so much .

-Xianghong Qi

On Wed, Nov 5, 2008 at 4:32 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Justin A. Lemkul wrote:
>
>>
>>
>> Justin A. Lemkul wrote:
>>
>>>
>>>
>>> xianghong qi wrote:
>>>
>>>> Thanks,  Justin:
>>>>
>>>> I use 4.0. Mine is here:
>>>> -------------------------------------------------------------------
>>>>  1  LJ-(SR)          2  Disper.-corr.    3  Coulomb-(SR)     4
>>>>  Coul.-recip.   5  Potential        6  Kinetic-En.      7  Total-Energy
>>>> 8  Temperature    9  Pressure-(bar)  10  Vir-XX          11  Vir-XY
>>>>  12  Vir-XZ        13  Vir-YX          14  Vir-YY          15  Vir-YZ
>>>>    16  Vir-ZX        17  Vir-ZY          18  Vir-ZZ          19
>>>>  Pres-XX-(bar)   20  Pres-XY-(bar)
>>>>  21  Pres-XZ-(bar)   22  Pres-YX-(bar)   23  Pres-YY-(bar)   24
>>>>  Pres-YZ-(bar)
>>>>  25  Pres-ZX-(bar)   26  Pres-ZY-(bar)   27  Pres-ZZ-(bar)   28
>>>>  #Surf*SurfTen
>>>>  29  Mu-X            30  Mu-Y            31  Mu-Z            32
>>>>  T-System
>>>>
>>>
> ...and I really should not hit "send" until I'm done thinking.  Are you
> applying pressure coupling in your simulation?  Under NVT conditions,
> parameters like Volume and Density are not written, since volume is constant
> and density doesn't mean much without constant pressure.
>
>
> -Justin
>
>
>>>  -Xianghong Qi
>>>>
>>>> On Wed, Nov 5, 2008 at 4:20 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>>>> jalemkul at vt.edu>> wrote:
>>>>
>>>>
>>>>
>>>>    xianghong qi wrote:
>>>>
>>>>        Hello, all:
>>>>
>>>>        I checked the mailing list. Looks like g_energy can calculate
>>>>        density vs time, but
>>>>        my g_energy doesn't have options like density, volume?  I am
>>>>        wondering how I can
>>>>        get my density vs time graph?  Any suggestion is appreciated.
>>>>        Thanks.
>>>>
>>>>
>>>>    Look more closely.  Both versions of Gromacs that I am currently
>>>>    using (3.3.3 and 4.0) have options for Density, Volume, and Box
>>>>    vectors as output from g_energy.
>>>>
>>>>    -Justin
>>>>
>>>>
>>>>        -Xianghong Qi
>>>>
>>>>
>>>>
>>>>        --         Some people make the world more special just by being
>>>> in it.
>>>>
>>>>
>>>>
>>>>  ------------------------------------------------------------------------
>>>>
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>>>>
>>>>    --     ========================================
>>>>
>>>>    Justin A. Lemkul
>>>>    Graduate Research Assistant
>>>>    Department of Biochemistry
>>>>    Virginia Tech
>>>>    Blacksburg, VA
>>>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>
>>>>    ========================================
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>>>>
>>>>
>>>>
>>>> --
>>>> Some people make the world more special just by being in it.
>>>>
>>>
>>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> 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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-- 
Some people make the world more special just by being in it.
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