[gmx-users] REMD - replicas sampling in temperatures beyond the assigned range

[Justin Lemkul]

On 6/30/16 8:46 AM, NISHA Prakash wrote:
> Dear all,
>
> I have conducted a 10ns REMD simulation for a protein ligand complex with
> the temperature range - 270 to 350 K, however the temperature distribution
> plot of the replicas show that the sampling has occurred at higher
> temperatures as well that is beyond 350K -
> Below is an excerpt from the temperature xvg file
>
>
> @    title "Gromacs Energies"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "(K)"
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "Temperature"
>     0.000000    0.000000
>    10.000000  350.997864
>    20.000000  353.618927
>    30.000000  350.068481
>    40.000000  353.921753
>    50.000000  359.485565
>    60.000000  353.463654
>    70.000000  352.015778
>    80.000000  350.657898
>    90.000000  351.927155
>   100.000000  354.539429
>   110.000000  354.287720
>   120.000000  349.436096
>   130.000000  352.960541
>   140.000000  351.631317
>   150.000000  354.217407
>   160.000000  350.185852
>   170.000000  350.294434
>   180.000000  350.980194
>   190.000000  350.914429
>                    ....
>                    ....
>  470.000000  349.224060
>   480.000000  350.819458
>   490.000000  348.541748
>   500.000000  350.393127
>   510.000000  398.775208
>   520.000000  444.802856
>   530.000000  470.899323
>   540.000000  466.652740
>   550.000000  465.600677
>   560.000000  469.225555
>   570.000000  470.548370
>   580.000000  470.011566
>   590.000000  470.643951
>   600.000000  472.433197
>   610.000000  470.451172
>   620.000000  469.991699
>   630.000000  469.073090
>   640.000000  467.259521
>   650.000000  464.561798
>   660.000000  468.416901
>   670.000000  468.754913
>   680.000000  469.259613
>   690.000000  467.641144
>   700.000000  468.542328
>
>
> Temperature coupling was done using Nose hoover algorithm.
>
> Does this imply the sampling is wrong or insufficent?
> Any help / suggestion is appreciated.
>

How large is your system, and what is it?  What were your (full) .mdp settings? 
The fact that your temperature started at 0 K and ramped up suggests that you 
did not equilibrate prior to the run, did not generate appropriate velocities, 
or did not continue properly.  The sudden jump in temperature later suggests 
instability, and could be due to incorrect settings.  N-H allows for large 
oscillations, but I wouldn't expect a stable system to that degree.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================