[gmx-users] Re: density vs time?

[Justin A. Lemkul]

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

========================================