[gmx-users] Understanding the results of NVT simulation

[Dallas Warren]

Would recommend that you actually plot the terms as a function of time, rather than just look at the averages and errors etc.  Much more information in doing that and you get a real feel for what is going on.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail. 

> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of
> Agnivo Gosai
> Sent: Thursday, 30 October 2014 4:38 AM
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Understanding the results of NVT simulation
> 
> 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.
> 
> 
> Thanks & Regards
> Agnivo Gosai
> Grad Student, Iowa State University.
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