[gmx-users] g_energy for density calculation

[Mark Abraham]

On 4/02/2012 1:10 AM, Chrisostomos Batistakis wrote:
>
>
> On Fri, Feb 3, 2012 at 2:38 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     On 4/02/2012 12:34 AM, Chrisostomos Batistakis wrote:
>>     Dear all
>>
>>     I would like to calculate the total density vs time in my system
>>     during an NPT simulation. I read the manual that I have to use
>>     the g_energy command in order to do that. My problem is  that 
>>     when I am running:
>>     */
>>     g_energy -f //a.edr /**/-s //b.tpr /**/-o //c.xvg/*
>>
>>     it gives me only these options:
>>
>>     /Select the terms you want from the following list by
>>     selecting either (part of) the name or the number or a combination.
>>     End your selection with an empty line or a zero.
>>     -------------------------------------------------------------------
>>       1  LJ-(SR)          2  Coulomb-(SR)     3  Position-Rest.   4 
>>     Potential
>>       5  Kinetic-En.      6  Total-Energy     7  Conserved-En.    8 
>>     Temperature
>>       9  Pressure        10  Constr.-rmsd    11  Vir-XX          12 
>>     Vir-XY
>>      13  Vir-XZ          14  Vir-YX          15  Vir-YY          16 
>>     Vir-YZ
>>      17  Vir-ZX          18  Vir-ZY          19  Vir-ZZ          20 
>>     Pres-XX
>>      21  Pres-XY         22  Pres-XZ         23  Pres-YX         24 
>>     Pres-YY
>>      25  Pres-YZ         26  Pres-ZX         27  Pres-ZY         28 
>>     Pres-ZZ
>>      29  #Surf*SurfTen   30  Mu-X            31  Mu-Y            32 
>>     Mu-Z
>>      33  T-System /
>>
>>
>>     Can anybody help me?
>
>     That's from an NVT simulation.
>
>     Mark
>
>
>
> Oh, sorry, I didn't imagine that it gives different options when doing 
> NVT or NPT.
> I really apologise :-)

No problem :) mdrun only writes relevant information, which can be 
valuable if you're producing terabytes of data from a a simulation! So 
no box size when it is constant :)

Mark
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