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