[gmx-users] Understanding the results of NVT simulation

[Dr. Vitaly Chaban]

On Wed, Oct 29, 2014 at 6:37 PM, Agnivo Gosai <agnivogromacs14 at gmail.com> wrote:
> Dear Users
>
> I did a NVT simulation with the following key parameters :-
>
> ; Temperature coupling
> tcoupl      = V-rescale                     ; modified Berendsen thermostat
> tc-grps     = DNA_Protein Water_and_ions    ; two coupling groups - more
> accurate
> tau_t       = 0.1     0.1                     ; time constant, in ps
> ref_t       = 300     300                     ; reference temperature, one
> for each group, in K
>
> The g_energy outputs for my nvt.edr file are as follows :-
>
> *For Temperature*
> Last energy frame read 500 time  100.000
>
> Statistics over 50001 steps [ 0.0000 through 100.0000 ps ], 1 data sets
> All statistics are over 10001 points
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> ------------------------------
> -------------------------------------------------
> Temperature                 299.638       0.32    4.75446    1.93228  (K)
>
> Question 1 : Is the drift of 1.93 K allowable ??
>
> *For Total Energy*
> Last energy frame read 500 time  100.000
>
> Statistics over 50001 steps [ 0.0000 through 100.0000 ps ], 1 data sets
> All statistics are over 10001 points
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Total Energy                -921661        560    8454.34    3197.77
> (kJ/mol)
>
> Question 2 : What is the physical significance of a high Err. Est and a
> high Tot-Drift ? I am unable to understand if my system is behaving

> properly or not.
>
> I use GROMACS 4.5.7 single precision.


According to my taste, everything goes allright. The drift is small
(what's the size of your system?), the error in energy is small (in
pct).

Go forward!

Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН