[gmx-users] question about energy fluctuation

[David van der Spoel]

Mark Abraham wrote:
> Qiao Baofu wrote:
>> Hi all,
>>
>> After running a MD of a system with about 17000 atoms, I calculated 
>> the potential and the total-energy:
>>
>> ************************************************************************************* 
>>
>> Last frame read 1557952 time 1557.952
>>
>> Statistics over 1557953 steps [ 0.0000 thru 1557.9520 ps ], 2 data sets
>>
>> Energy                      Average       RMSD     Fluct.      Drift  
>> Tot-Drift
>> ------------------------------------------------------------------------------- 
>>
>> Potential                   -273047    626.559    611.258  -0.305998   
>> -476.731
>> Total-Energy                -184656    839.662    828.307  -0.305999   
>> -476.731
>> ************************************************************************************* 
>>
>>
>> I found that the Fluct./Average is 0.45% (Total-Energy), 
>> 0.22%(Potential). In the simulation, the time step is 0.001ps, and I 
>> saved the energy every step.
>> On the other hand, on page 98 of the book "Computer Simulation of 
>> Liquids" (M. P. Allen & D. J. Tildesley), it is said "For a simple 
>> Lennard-Jones system, fluctuation of order 1 part in 10^4 are 
>> generally considered to be acceptable." 
> 
> This book was written nearly 20 years ago, so take with a "grain of 
> salt" its advice on "general acceptability".
> 
> Was this a simple Lennard-Jones system? If not, you are comparing apples 
> and oranges anyway.

The book is fine, but limited to LJ systems. Therefore Mark's question 
is important.

> 
>> The ratio obtained from Gromacs are quite bigger.  Therefore, I want 
>> to know if there are any standard for different system to check 
>> whether the system are accetable or not.
>>
>>
>> PS: Another question: I found only when the energy data are divided by 
>> the number of the molecules, the obtained result are consistent with 
>> the date in some related papers. In Gromacs, the unit of energy is 
>> KJ/mol. If divided by the number of molecules, how to consider the unit?
> 
> kJ/mol per molecule? :-P
> 
> The conversion is straightforward, but you may find it easier 
> conceptually to convert your other sources into kJ/mol.

You can divide by the number of molecules using g_energy -nmol.
The reason GROMACS doesn't do it for you is that it is well defined only 
for monomolecular systems. The energy you get is hence kJ/mol system. 
Where system is your complete system, be it 125 argon atoms or a large 
biological complex.


> 
> Mark
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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