[gmx-users] Re: Accuracy of simulations

[David van der Spoel]

najwa drici wrote:
> 
>     I made a MD simulation  of solvated protein and i have the out put
>     file md.log , I took the part  of " R M S - F L U C T U A T I O N S "
> 
> 
>     in order to calculating the ratio R = Δ E_tot /Δ E_kin who should be
>     less than 0.05
> 
> R = Δ E_tot /Δ E_kin   = 3.33405e+002/8.21064e+001  = 4.0606 

This looks to much, but you should probably verify that your simulation
is in equilibrium first.
Please put further questions on the mailing list.

>  
>  
> my questionsa are:
>  
>  
> is R=4.0606  a percentage  ? i.e  can i  write R= 0.040606 ???
>  
> is my simulation is accurate ?
> 
>  
>  this is my  md.log file
> <======  ###############################  ==>
>  <====  R M S - F L U C T U A T I O N S  ====>
>  <==  ###############################  ======>
>    Energies (kJ/mol)
>        G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>    2.53814e+001   1.57197e+001   1.20353e+001   1.13133e+001   3.16586e+001
>         LJ (SR)       Coulomb (SR)   Coulomb (LR)      
> Potential          Kinetic En.
>    2.54693e+002   4.29057e+002   3.23823e+002   3.41410e+002   8.21064e+001
>    Total Energy    Temperature      Pressure (bar)
>    3.33405e+002   2.27536e+000   3.26751e+002
>    Total Virial (kJ/mol)
>    6.61328e+002   4.23233e+002   4.20276e+002
>    4.23314e+002   6.56348e+002   4.19655e+002
>    4.19582e+002   4.18954e+002   6.49220e+002
>    Pressure (bar)
>    4.91246e+002   3.17484e+002   3.15086e+002
>    3.17539e+002   4.88127e+002   3.15631e+002
>    3.14572e+002   3.15128e+002   4.82007e+002
>    Total Dipole (Debye)
>    2.81842e+001   3.19246e+001   2.69345e+001
>       T-Protein  T-Non-Protein
>    1.34141e+001   2.30678e+000
>  
> thank you
> 
> 
> 
> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se